[CHNOSZ-commits] r508 - in pkg/CHNOSZ: . R demo inst inst/extdata/abundance inst/extdata/protein inst/extdata/thermo man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Oct 19 08:22:15 CEST 2019
Author: jedick
Date: 2019-10-19 08:22:14 +0200 (Sat, 19 Oct 2019)
New Revision: 508
Removed:
pkg/CHNOSZ/R/yeast.R
pkg/CHNOSZ/demo/revisit.R
pkg/CHNOSZ/demo/yeastgfp.R
pkg/CHNOSZ/inst/extdata/abundance/TBD+05.csv
pkg/CHNOSZ/inst/extdata/abundance/yeastgfp.csv.xz
pkg/CHNOSZ/inst/extdata/protein/Sce.csv.xz
pkg/CHNOSZ/man/yeast.Rd
pkg/CHNOSZ/tests/testthat/test-yeast.aa.R
pkg/CHNOSZ/tests/testthat/test-yeastgfp.R
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/demo/wjd.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/thermo/protein.csv
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/add.protein.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/tests/testthat/test-wjd.R
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/mklinks.sh
Log:
remove yeast.aa(), yeastgfp() and related data files
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/DESCRIPTION 2019-10-19 06:22:14 UTC (rev 508)
@@ -1,6 +1,6 @@
-Date: 2019-09-10
+Date: 2019-10-19
Package: CHNOSZ
-Version: 1.3.3-4
+Version: 1.3.3-5
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/NAMESPACE 2019-10-19 06:22:14 UTC (rev 508)
@@ -9,7 +9,7 @@
"describe.property", "describe.basis", "equilibrate",
"aminoacids", "ZC.col",
"pinfo", "protein.length", "protein.formula",
- "read.fasta", "protein.basis", "yeastgfp", "yeast.aa", "add.protein",
+ "read.fasta", "protein.basis", "add.protein",
"unitize", "revisit", "seq2aa", "findit",
"thermo.refs", "mod.obigt", "today",
# examples
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/R/examples.R 2019-10-19 06:22:14 UTC (rev 508)
@@ -11,7 +11,7 @@
"util.water", "taxonomy", "info", "retrieve", "add.obigt", "protein.info",
"hkf", "water", "IAPWS95", "subcrt", "berman",
"makeup", "basis", "swap.basis", "species", "affinity", "solubility", "equilibrate",
- "diagram", "buffer", "nonideal", "NaCl", "add.protein", "protein", "ionize.aa", "yeast.aa",
+ "diagram", "buffer", "nonideal", "NaCl", "add.protein", "protein", "ionize.aa",
"objective", "revisit", "EOSregress", "wjd")
plot.it <- FALSE
if(is.character(save.png))
@@ -28,7 +28,7 @@
}
demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
- "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "glycinate",
+ "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "glycinate",
"mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "wjd",
"bugstab", "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "aluminum", "bison", "AkDi"), save.png=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/R/info.R 2019-10-19 06:22:14 UTC (rev 508)
@@ -11,8 +11,10 @@
info <- function(species=NULL, state=NULL, check.it=TRUE) {
## return information for one or more species in thermo$obigt
+ thermo <- get("thermo", CHNOSZ)
+ # that should give us the data, not the thermo() function 20190928
+ if(is.function(thermo)) stop("CHNOSZ package data is not available; use reset() or library(CHNOSZ) to load it")
## if no species are requested, summarize the available data 20101129
- thermo <- get("thermo", CHNOSZ)
if(is.null(species)) {
message("info: 'species' is NULL; summarizing information about thermodynamic data...")
message(paste("thermo$obigt has", nrow(thermo$obigt[thermo$obigt$state=="aq", ]), "aqueous,",
@@ -21,10 +23,6 @@
nrow(thermo$element), ", buffers: ", length(unique(thermo$buffers$name)), sep=""))
message(paste("number of proteins in thermo$protein is", nrow(thermo$protein), "from",
length(unique(thermo$protein$organism)), "organisms"))
- # print information about Sce.csv
- yeast.aa()
- # print information about yeastgfp.csv
- yeastgfp()
return()
}
## run info.numeric or info.character depending on the input type
Deleted: pkg/CHNOSZ/R/yeast.R
===================================================================
--- pkg/CHNOSZ/R/yeast.R 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/R/yeast.R 2019-10-19 06:22:14 UTC (rev 508)
@@ -1,104 +0,0 @@
-# CHNOSZ/yeast.R
-# get amino acid compositions of proteins from Saccharomyces cerevisiae
-
-yeast.aa <- function(protein=NULL) {
- # return the composition of one or more proteins from S. cerevisiae (Sce)
- # extracted from get.protein 20120519
- datapath <- paste("extdata/protein/Sce.csv.xz", sep="")
- datafile <- system.file(datapath, package="CHNOSZ")
- if(datafile=="") stop(paste("missing", datapath))
- mydata <- read.csv(datafile, as.is=TRUE)
- # if protein is not supplied, just give some information about the datafile
- if(is.null(protein)) {
- message("yeast.aa: ", datapath, " has data for ", nrow(mydata), " proteins")
- return(invisible())
- }
- # which columns to search for matches
- searchcols <- c("ORF", "SGDID", "GENE")
- # which columns have the amino acids, in the order of thermo$protein
- iaa <- match(toupper(aminoacids(3)), toupper(colnames(mydata)))
- # iterate over a list
- waslist <- TRUE
- out <- list()
- if(!is.list(protein)) {
- waslist <- FALSE
- protein <- list(protein)
- }
- for(i in 1:length(protein)) {
- # find the matches
- imatch <- rep(NA, length(protein[[i]]))
- for(cname in searchcols) {
- icol <- match(cname, colnames(mydata))
- if(is.na(icol)) next
- iimatch <- match(protein[[i]], mydata[, icol])
- imatch[!is.na(iimatch)] <- iimatch[!is.na(iimatch)]
- }
- # report and remember the unsuccessful matches
- if(all(is.na(imatch))) stop("no proteins found!")
- inotmatch <- which(is.na(imatch))
- if(length(inotmatch) > 0) {
- if(length(inotmatch)==1) verb <- " was" else verb <- " were"
- message("yeast.aa: ", paste(protein[[i]][inotmatch], collapse=" "), verb, " not matched")
- }
- aa <- data.frame(mydata[imatch, iaa])
- # add the identifying columns
- ref <- mydata$SGDID[imatch]
- abbrv <- mydata$GENE[imatch]
- chains <- rep(1, length(protein[[i]]))
- chains[inotmatch] <- NA
- org <- rep("Sce", length(protein[[i]]))
- precols <- data.frame(protein[[i]], organism=org, ref, abbrv, chains, stringsAsFactors=FALSE)
- colnames(precols)[1] <- "protein"
- colnames(aa) <- aminoacids(3)
- aa <- cbind(precols, aa)
- out <- c(out, list(aa))
- }
- # done!
- if(!waslist) return(out[[1]])
- else return(out)
-}
-
-# yeastgfp: protein localization and abundance from yeastgfp.csv
-yeastgfp <- function(location=NULL, exclusive=TRUE) {
- # return a list of ORFs and protein abundances for a subcellular location
- # using data from the YeastGFP project
- # (yeastgfp.csv data file added to CHNOSZ_0.8, 20090422)
- ypath <- "extdata/abundance/yeastgfp.csv.xz"
- yfile <- system.file(ypath, package="CHNOSZ")
- # yeastgfp preprocessing
- ygfp <- read.csv(yfile)
- # convert factors to numeric w/o NA coercion warnings
- ygfp$abundance <- as.numeric.nowarn(as.character(ygfp$abundance))
- # if location is NULL, just report on the content of the file
- # and return the names of the locations
- if(is.null(location)) {
- message("yeastgfp: ", ypath, " has ", nrow(ygfp), " localizations and ",
- length(ygfp$abundance[!is.na(ygfp$abundance)]), " abundances")
- return(invisible(colnames(ygfp)[6:28]))
- }
- # iterate over multiple locations
- out <- list()
- for(i in 1:length(location)) {
- # what location do we want?
- ncol <- match(location[i], colnames(ygfp)[6:28]) + 5
- if(is.na(ncol)) ncol <- agrep(location[i], colnames(ygfp)[6:28])[1] + 5
- if(is.na(ncol)) stop(paste(location[i], "is not one of the subcellular locations in", ypath))
- thisygfp <- ygfp[, ncol]
- if(exclusive) {
- # find the number of localizations of each ORF
- localizations <- numeric(nrow(ygfp))
- for(j in 6:28) localizations <- localizations + as.logical(ygfp[,j])
- if(all(localizations[thisygfp] > 1)) message("yeastgfp: no exclusive localization found for ",location[i],
- " ... using non-exclusive localizations",sep="")
- else thisygfp <- thisygfp & ! localizations > 1
- }
- protein <- as.character(ygfp$yORF[thisygfp])
- abundance <- ygfp$abundance[thisygfp]
- if(length(location)==1) out <- list(protein=protein, abundance=abundance)
- else {
- out$protein <- c(out$protein, list(protein))
- out$abundance <- c(out$abundance, list(abundance))
- }
- }
- return(out)
-}
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/demo/00Index 2019-10-19 06:22:14 UTC (rev 508)
@@ -4,12 +4,10 @@
NaCl Equilibrium constant for aqueous NaCl dissociation
density Density of H2O, inverted from IAPWS-95 equations
ORP Temperature dependence of oxidation-reduction potential for redox standards
-revisit Coefficient of variation of metastable equilibrium activities of proteins
findit Minimize the standard deviation of logarithms of activities of sulfur species
ionize ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK
buffer Minerals and aqueous species as buffers of hydrogen fugacity
protbuff Chemical activities buffered by thiol peroxidases or sigma factors
-yeastgfp Subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams
glycinate Metal-glycinate complexes
mosaic Eh-pH diagram for iron oxides, sulfides and carbonate with two sets of changing basis species
copper Another example of mosaic(): complexation of copper with glycine species
Deleted: pkg/CHNOSZ/demo/revisit.R
===================================================================
--- pkg/CHNOSZ/demo/revisit.R 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/demo/revisit.R 2019-10-19 06:22:14 UTC (rev 508)
@@ -1,38 +0,0 @@
-## Demo for revisit(): CV of equilibrium activities of proteins in
-## subcellular compartment of S. cerevisiae
-
-# get the proteins in the requested location
-loc <- "cell.periphery"
-y <- yeastgfp(loc)
-# get the amino acid compositions of the proteins
-aa <- yeast.aa(y$protein)
-# don't use those with NA abundance or sequence
-ina <- is.na(y$abundance) | is.na(aa$chains)
-aa <- aa[!ina, ]
-# add these proteins to CHNOSZ's inventory
-ip <- add.protein(aa)
-# set up a the chemical system
-basis("CHNOS+")
-# calculate affinities of formation in logfO2 space
-a <- affinity(O2=c(-85, -60), iprotein=ip)
-# show the equilibrium activities
-opar <- par(mfrow=c(2, 2))
-e <- equilibrate(a, loga.balance=0, normalize=TRUE)
-diagram(e, names=FALSE)
-# make a title
-expr <- as.expression(substitute(x~loc~"proteins in"~
- italic("S. cerevisiae"), list(x=length(ip), loc=loc)))
-mtitle(c("Equilibrium activities of", expr))
-# show the coefficient of variation
-revisit(e, "CV")
-mtitle(c("CV of equilibrium activities of", expr))
-# calculate affinities in logfO2-logaH2O space
-a <- affinity(O2=c(-85, -65), H2O=c(-5, 5), iprotein=ip)
-# show the predominances
-diagram(a, normalize=TRUE, fill="heat")
-# calculate the equilibrium activities
-e <- equilibrate(a, loga.balance=0, normalize=TRUE)
-# show the coefficient of variation
-r <- revisit(e, "CV")
-mtitle(c("CV of equilibrium activities of", expr))
-par(opar)
Modified: pkg/CHNOSZ/demo/wjd.R
===================================================================
--- pkg/CHNOSZ/demo/wjd.R 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/demo/wjd.R 2019-10-19 06:22:14 UTC (rev 508)
@@ -33,37 +33,3 @@
text(7, log10(Xs[, 1]), dlen$formula, adj=1)
title(main="Prebiological atmospheres (Dayhoff et al., 1964)")
#dev.off()
-
-## run.wjd with proteins: cell periphery of yeast
-# get the proteins in the requested location
-y <- yeastgfp("cell.periphery")
-# get the amino acid compositions of the proteins
-aa <- yeast.aa(y$protein)
-# don't use those with NA abundance or sequence
-ina <- is.na(y$abundance) | is.na(aa$chains)
-aa <- aa[!ina, ]
-# let's try normalizing the proteins to single residues
-# columns 6:25 are the actual amino acid counts
-aa.625 <- aa[, 6:25]
-aa[, 6:25] <- aa.625 / rowSums(aa.625)
-# add proteins to thermo$protein
-add.protein(aa)
-# add proteins to thermo$obigt
-iobigt <- info(paste(aa$protein, aa$organism, sep="_"))
-# use equal initial abundances, with total equal to yeastGFP abundances
-Y <- rep(mean(y$abundance[!ina]), length(y$abundance[!ina]))
-# run the Gibbs energy minimization
-w <- run.wjd(iobigt, Y=Y, imax=100)
-# make a log-log plot
-plot(log10(y$abundance[!ina]), log10(w$X), xlim=c(1.5, 5), ylim=c(1.5, 5),
- xlab="log10(abundance) reported in YeastGFP study",
- ylab="log10(abundance) calculated using Gibbs energy minimization")
-# get the element potentials (tolerating "close enough" to equilibrium)
-emu <- equil.potentials(w, tol=1e7)
-# then the logarithms of activities of the basis species
-basis("CHNOS")
-bl <- basis.logact(emu)
-# make a title and legend
-title(main="Relative abundances of proteins: yeast cell periphery")
-basis(names(bl), bl)
-legend("topleft", describe.basis(digits=2))
Deleted: pkg/CHNOSZ/demo/yeastgfp.R
===================================================================
--- pkg/CHNOSZ/demo/yeastgfp.R 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/demo/yeastgfp.R 2019-10-19 06:22:14 UTC (rev 508)
@@ -1,71 +0,0 @@
-## Oxygen fugacity - activity of H2O predominance
-## diagrams for proteologs for 23 YeastGFP localizations
-# use superseded properties of [Met], [Gly], and [UPBB] (Dick et al., 2006)
-add.obigt("OldAA")
-# arranged by decreasing metastability:
-# order of this list of locations is based on the
-# (dis)appearance of species on the current set of diagrams
-names <- c("vacuole", "early.Golgi", "ER", "lipid.particle",
- "cell.periphery", "ambiguous", "Golgi", "mitochondrion",
- "bud", "actin", "cytoplasm", "late.Golgi",
- "endosome", "nucleus", "vacuolar.membrane", "punctate.composite",
- "peroxisome", "ER.to.Golgi", "nucleolus", "spindle.pole",
- "nuclear.periphery", "bud.neck", "microtubule")
-nloc <- c(4, 5, 3, 4, 4, 3)
-# define the system
-basis("CHNOS+")
-# get protein names and abundances in each location
-gfp <- yeastgfp(names)
-# get amino acid compositions of proteins
-aa <- yeast.aa(gfp$protein)
-# calculate average amino acid compositions
-for(i in 1:length(names)) {
- avgaa <- aasum(aa[[i]], gfp$abundance[[i]], average=TRUE, protein=names[i])
- add.protein(avgaa)
-}
-species(names, "Sce")
-a <- affinity(H2O=c(-5, 0, 256), O2=c(-80, -66, 256))
-# setup the plot
-opar <- par(no.readonly = TRUE)
-layout(matrix(c(1, 1,2:7), byrow=TRUE, nrow=4), heights=c(0.7, 3, 3, 3))
-par(mar=c(0, 0, 0, 0))
-plot.new()
-text(0.5, 0.7, expression("Proteins in subcellular locations of"~italic("S. cerevisiae")~"(Dick, 2009)"), cex=1.5)
-text(0.5, 0.2, describe.basis(ibasis=c(1, 3, 4, 6), oneline=TRUE), cex=1.5)
-par(mar=c(3, 4, 1, 1), xpd=TRUE)
-fill <- heat.colors(length(names))
-inames <- 1:length(names)
-for(i in 1:length(nloc)) {
- diagram(a, normalize=TRUE, names=names[inames], groups=as.list(inames),
- fill=fill[inames], cex.axis=0.75, cex.names=1.2)
- label.plot(letters[i], xfrac=0.95, yfrac=0.9, paren=TRUE, italic=TRUE)
- title(main=paste(length(inames), "locations"))
- # take out the stable species
- inames <- inames[-(1:nloc[i])]
-}
-# return to plot defaults
-layout(matrix(1))
-par(xpd=FALSE)
-par(opar)
-
-## Localizations and abundances of proteins from YeastGFP are used here
-## to calculate an abundance-weighted average of amino acid compositions of proteins
-## in different subcellular compartments of yeast.
-## This figure is similar to Fig. 3 of Dick (2009).
-locations <- yeastgfp()
-gfp <- yeastgfp(locations)
-aa <- yeast.aa(gfp$protein)
-for(i in 1:length(locations)) {
- avgaa <- aasum(aa[[i]], gfp$abundance[[i]], average=TRUE, protein=locations[i])
- add.protein(avgaa)
-}
-basis("CHNOS+")
-species(locations, "Sce")
-a <- affinity(O2=c(-82, -65))
-e <- equilibrate(a, loga.balance=0, normalize=TRUE)
-mycolor <- topo.colors(length(locations))
-diagram(e, names=locations, ylim=c(-5, -3), col=mycolor, lwd=2)
-title(main=expression("Proteins in subcellular locations of"~italic("S. cerevisiae")))
-
-# reset thermodynamic database
-reset()
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/inst/NEWS 2019-10-19 06:22:14 UTC (rev 508)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.3-4 (2019-09-10)
+CHANGES IN CHNOSZ 1.3.3-5 (2019-10-19)
--------------------------------------
- describe.reaction(): revert the change of using a double arrow. The
@@ -13,6 +13,10 @@
- Fix bug in unexported function obigt2eos(): lambda (exponent in heat
capacity equation) was incorrectly going through a units conversion.
+- Remove yeastgfp(), yeast.aa(), Sce.csv.xz, yeastgfp.csv.xz, and other
+ associated files. The data files and functions have been moved to the
+ JMDplots package (https://github.com/jedick/JMDplots).
+
CHANGES IN CHNOSZ 1.3.3 (2019-08-02)
------------------------------------
Deleted: pkg/CHNOSZ/inst/extdata/abundance/TBD+05.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/abundance/TBD+05.csv 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/inst/extdata/abundance/TBD+05.csv 2019-10-19 06:22:14 UTC (rev 508)
@@ -1,393 +0,0 @@
-protein,Clim.aerobic.down,Clim.aerobic.up,Clim.anaerobic.down,Clim.anaerobic.up
-YBL029W,TRUE,FALSE,FALSE,FALSE
-YBL095W,TRUE,FALSE,FALSE,FALSE
-YBR151W,TRUE,FALSE,FALSE,FALSE
-YCL025C,TRUE,FALSE,FALSE,TRUE
-YCR043C,TRUE,FALSE,FALSE,FALSE
-YCR102C,TRUE,FALSE,FALSE,FALSE
-YDR309C,TRUE,FALSE,FALSE,FALSE
-YDR352W,TRUE,FALSE,FALSE,FALSE
-YDR533C,TRUE,FALSE,FALSE,FALSE
-YEL016C,TRUE,FALSE,FALSE,FALSE
-YER001W,TRUE,FALSE,FALSE,FALSE
-YER028C,TRUE,FALSE,FALSE,FALSE
-YER053C,TRUE,FALSE,FALSE,FALSE
-YER124C,TRUE,FALSE,FALSE,FALSE
-YFL025C,TRUE,FALSE,FALSE,FALSE
-YFL026W,TRUE,FALSE,FALSE,FALSE
-YGL065C,TRUE,FALSE,FALSE,FALSE
-YGR041W,TRUE,FALSE,FALSE,FALSE
-YGR125W,TRUE,FALSE,FALSE,FALSE
-YGR192C,TRUE,FALSE,FALSE,FALSE
-YHR048W,TRUE,FALSE,FALSE,FALSE
-YHR049W,TRUE,FALSE,FALSE,FALSE
-YHR179W,TRUE,FALSE,FALSE,FALSE
-YHR210C,TRUE,FALSE,FALSE,FALSE
-YIL111W,TRUE,FALSE,FALSE,FALSE
-YJL212C,TRUE,FALSE,FALSE,FALSE
-YJL213W,TRUE,FALSE,FALSE,FALSE
-YJR030C,TRUE,FALSE,FALSE,FALSE
-YKL043W,TRUE,FALSE,FALSE,FALSE
-YKL062W,TRUE,FALSE,FALSE,FALSE
-YKL209C,TRUE,FALSE,FALSE,FALSE
-YKR093W,TRUE,FALSE,FALSE,FALSE
-YLL028W,TRUE,FALSE,FALSE,FALSE
-YLR108C,TRUE,FALSE,FALSE,FALSE
-YLR179C,TRUE,FALSE,FALSE,FALSE
-YLR460C,TRUE,FALSE,FALSE,FALSE
-YMR057C,TRUE,FALSE,FALSE,FALSE
-YMR269W,TRUE,FALSE,FALSE,FALSE
-YMR285C,TRUE,FALSE,FALSE,FALSE
-YNL066W,TRUE,FALSE,FALSE,FALSE
-YNL134C,TRUE,FALSE,FALSE,FALSE
-YNR032C-A,TRUE,FALSE,FALSE,FALSE
-YOL136C,TRUE,FALSE,FALSE,FALSE
-YOR171C,TRUE,FALSE,FALSE,FALSE
-YPL095C,TRUE,FALSE,FALSE,FALSE
-YPR013C,TRUE,FALSE,FALSE,FALSE
-YPR106W,TRUE,FALSE,FALSE,FALSE
-YPR138C,TRUE,FALSE,FALSE,FALSE
-YAL054C,FALSE,TRUE,FALSE,FALSE
-YAR068W,FALSE,TRUE,FALSE,FALSE
-YBR026C,FALSE,TRUE,FALSE,FALSE
-YBR046C,FALSE,TRUE,FALSE,FALSE
-YBR068C,FALSE,TRUE,FALSE,FALSE
-YBR072W,FALSE,TRUE,FALSE,FALSE
-YBR116C,FALSE,TRUE,FALSE,FALSE
-YBR117C,FALSE,TRUE,FALSE,FALSE
-YBR150C,FALSE,TRUE,FALSE,FALSE
-YBR157C,FALSE,TRUE,FALSE,FALSE
-YBR230C,FALSE,TRUE,FALSE,FALSE
-YBR295W,FALSE,TRUE,FALSE,FALSE
-YCR010C,FALSE,TRUE,FALSE,FALSE
-YCR018C,FALSE,TRUE,FALSE,FALSE
-YDL009C,FALSE,TRUE,FALSE,FALSE
-YDL049C,FALSE,TRUE,FALSE,FALSE
-YDL085W,FALSE,TRUE,FALSE,FALSE
-YDL204W,FALSE,TRUE,FALSE,FALSE
-YDL214C,FALSE,TRUE,FALSE,FALSE
-YDL223C,FALSE,TRUE,FALSE,FALSE
-YDR018C,FALSE,TRUE,FALSE,FALSE
-YDR034W-B,FALSE,TRUE,FALSE,FALSE
-YDR070C,FALSE,TRUE,FALSE,FALSE
-YDR077W,FALSE,TRUE,FALSE,FALSE
-YDR216W,FALSE,TRUE,FALSE,FALSE
-YDR256C,FALSE,TRUE,FALSE,FALSE
-YDR380W,FALSE,TRUE,FALSE,FALSE
-YDR384C,FALSE,TRUE,FALSE,FALSE
-YDR453C,FALSE,TRUE,FALSE,FALSE
-YDR536W,FALSE,TRUE,FALSE,FALSE
-YEL041W,FALSE,TRUE,FALSE,FALSE
-YEL057C,FALSE,TRUE,FALSE,FALSE
-YER015W,FALSE,TRUE,FALSE,FALSE
-YER024W,FALSE,TRUE,FALSE,FALSE
-YER065C,FALSE,TRUE,FALSE,FALSE
-YER103W,FALSE,TRUE,FALSE,FALSE
-YER121W,FALSE,TRUE,FALSE,FALSE
-YFL011W,FALSE,TRUE,FALSE,FALSE
-YFL030W,FALSE,TRUE,FALSE,FALSE
-YGL080W,FALSE,TRUE,FALSE,FALSE
-YGL117W,FALSE,TRUE,FALSE,FALSE
-YGL205W,FALSE,TRUE,FALSE,FALSE
-YGL208W,FALSE,TRUE,FALSE,FALSE
-YGR043C,FALSE,TRUE,FALSE,FALSE
-YGR067C,FALSE,TRUE,FALSE,FALSE
-YGR201C,FALSE,TRUE,FALSE,FALSE
-YGR230W,FALSE,TRUE,FALSE,FALSE
-YGR236C,FALSE,TRUE,FALSE,FALSE
-YGR250C,FALSE,TRUE,FALSE,FALSE
-YGR256W,FALSE,TRUE,FALSE,FALSE
-YHL032C,FALSE,TRUE,FALSE,FALSE
-YHR015W,FALSE,TRUE,FALSE,FALSE
-YHR096C,FALSE,TRUE,FALSE,FALSE
-YHR209W,FALSE,TRUE,FALSE,FALSE
-YIL107C,FALSE,TRUE,FALSE,FALSE
-YIL117C,FALSE,TRUE,FALSE,FALSE
-YIL136W,FALSE,TRUE,FALSE,FALSE
-YIL155C,FALSE,TRUE,FALSE,FALSE
-YIL160C,FALSE,TRUE,FALSE,FALSE
-YIR016W,FALSE,TRUE,FALSE,FALSE
-YIR038C,FALSE,TRUE,FALSE,FALSE
-YJL037W,FALSE,TRUE,FALSE,FALSE
-YJL045W,FALSE,TRUE,FALSE,FALSE
-YJL089W,FALSE,TRUE,FALSE,FALSE
-YJL137C,FALSE,TRUE,FALSE,FALSE
-YJL144W,FALSE,TRUE,FALSE,FALSE
-YJL153C,FALSE,TRUE,FALSE,FALSE
-YJL161W,FALSE,TRUE,FALSE,FALSE
-YJL185C,FALSE,TRUE,FALSE,FALSE
-YJL191W,FALSE,TRUE,FALSE,FALSE
-YJL216C,FALSE,TRUE,FALSE,FALSE
-YJL217W,FALSE,TRUE,FALSE,FALSE
-YJR019C,FALSE,TRUE,FALSE,FALSE
-YJR094C,FALSE,TRUE,FALSE,FALSE
-YJR095W,FALSE,TRUE,FALSE,FALSE
-YJR096W,FALSE,TRUE,FALSE,FALSE
-YJR109C,FALSE,TRUE,FALSE,FALSE
-YJR156C,FALSE,TRUE,FALSE,FALSE
-YKL026C,FALSE,TRUE,FALSE,FALSE
-YKL093W,FALSE,TRUE,FALSE,FALSE
-YKL107W,FALSE,TRUE,FALSE,FALSE
-YKL138C,FALSE,TRUE,FALSE,FALSE
-YKL171W,FALSE,TRUE,FALSE,FALSE
-YKL187C,FALSE,TRUE,FALSE,FALSE
-YKR009C,FALSE,TRUE,FALSE,FALSE
-YKR049C,FALSE,TRUE,FALSE,FALSE
-YKR067W,FALSE,TRUE,FALSE,FALSE
-YKR075C,FALSE,TRUE,FALSE,FALSE
-YKR076W,FALSE,TRUE,FALSE,FALSE
-YKR091W,FALSE,TRUE,FALSE,FALSE
-YLR174W,FALSE,TRUE,FALSE,FALSE
-YLR194C,FALSE,TRUE,FALSE,FALSE
-YLR284C,FALSE,TRUE,FALSE,FALSE
-YLR307W,FALSE,TRUE,FALSE,FALSE
-YLR377C,FALSE,TRUE,FALSE,FALSE
-YLR411W,FALSE,TRUE,FALSE,FALSE
-YML042W,FALSE,TRUE,FALSE,FALSE
-YML054C,FALSE,TRUE,FALSE,FALSE
-YML122C,FALSE,TRUE,FALSE,FALSE
-YML128C,FALSE,TRUE,FALSE,FALSE
-YMR006C,FALSE,TRUE,FALSE,FALSE
-YMR011W,FALSE,TRUE,TRUE,FALSE
-YMR095C,FALSE,TRUE,FALSE,FALSE
-YMR096W,FALSE,TRUE,FALSE,FALSE
-YMR107W,FALSE,TRUE,FALSE,FALSE
-YMR118C,FALSE,TRUE,FALSE,FALSE
-YMR174C,FALSE,TRUE,FALSE,FALSE
-YMR175W,FALSE,TRUE,FALSE,FALSE
-YMR191W,FALSE,TRUE,FALSE,FALSE
-YMR280C,FALSE,TRUE,FALSE,FALSE
-YMR303C,FALSE,TRUE,FALSE,FALSE
-YNL009W,FALSE,TRUE,FALSE,FALSE
-YNL012W,FALSE,TRUE,FALSE,FALSE
-YNL194C,FALSE,TRUE,FALSE,FALSE
-YNL195C,FALSE,TRUE,FALSE,FALSE
-YNL202W,FALSE,TRUE,FALSE,FALSE
-YNL270C,FALSE,TRUE,FALSE,FALSE
-YNL335W,FALSE,TRUE,FALSE,FALSE
-YNR002C,FALSE,TRUE,FALSE,FALSE
-YNR056C,FALSE,TRUE,FALSE,FALSE
-YNR058W,FALSE,TRUE,FALSE,FALSE
-YNR060W,FALSE,TRUE,FALSE,FALSE
-YOL083W,FALSE,TRUE,FALSE,FALSE
-YOL101C,FALSE,TRUE,FALSE,FALSE
-YOL126C,FALSE,TRUE,FALSE,FALSE
-YOL147C,FALSE,TRUE,FALSE,FALSE
-YOR100C,FALSE,TRUE,FALSE,FALSE
-YOR120W,FALSE,TRUE,FALSE,FALSE
-YOR180C,FALSE,TRUE,FALSE,FALSE
-YOR388C,FALSE,TRUE,FALSE,FALSE
-YPL036W,FALSE,TRUE,FALSE,FALSE
-YPL109C,FALSE,TRUE,FALSE,FALSE
-YPL113C,FALSE,TRUE,FALSE,FALSE
-YPL134C,FALSE,TRUE,FALSE,FALSE
-YPL147W,FALSE,TRUE,FALSE,FALSE
-YPL156C,FALSE,TRUE,FALSE,FALSE
-YPL186C,FALSE,TRUE,FALSE,FALSE
-YPL201C,FALSE,TRUE,FALSE,FALSE
-YPL230W,FALSE,TRUE,FALSE,FALSE
-YPL276W,FALSE,TRUE,FALSE,FALSE
-YPR001W,FALSE,TRUE,FALSE,FALSE
-YPR002W,FALSE,TRUE,FALSE,FALSE
-YPR006C,FALSE,TRUE,FALSE,FALSE
-YPR026W,FALSE,TRUE,FALSE,FALSE
-YPR182W,FALSE,TRUE,FALSE,FALSE
-YAL024C,FALSE,FALSE,TRUE,FALSE
-YAL027W,FALSE,FALSE,TRUE,FALSE
-YAL058W,FALSE,FALSE,TRUE,FALSE
-YAR003W,FALSE,FALSE,TRUE,FALSE
-YAR008W,FALSE,FALSE,TRUE,FALSE
-YAR033W,FALSE,FALSE,TRUE,FALSE
-YBL025W,FALSE,FALSE,TRUE,FALSE
-YBL060W,FALSE,FALSE,TRUE,FALSE
-YBL075C,FALSE,FALSE,TRUE,FALSE
-YBL078C,FALSE,FALSE,TRUE,FALSE
-YBL079W,FALSE,FALSE,TRUE,FALSE
-YBR063C,FALSE,FALSE,TRUE,FALSE
-YBR217W,FALSE,FALSE,TRUE,FALSE
-YCL010C,FALSE,FALSE,TRUE,FALSE
-YCL024W,FALSE,FALSE,TRUE,FALSE
-YCL027W,FALSE,FALSE,TRUE,FALSE
-YCL055W,FALSE,FALSE,TRUE,FALSE
-YCR019W,FALSE,FALSE,TRUE,FALSE
-YDL024C,FALSE,FALSE,TRUE,FALSE
-YDL039C,FALSE,FALSE,TRUE,FALSE
-YDR030C,FALSE,FALSE,TRUE,FALSE
-YDR033W,FALSE,FALSE,TRUE,FALSE
-YDR111C,FALSE,FALSE,TRUE,FALSE
-YDR118W,FALSE,FALSE,TRUE,FALSE
-YDR123C,FALSE,FALSE,TRUE,FALSE
-YDR200C,FALSE,FALSE,TRUE,FALSE
-YDR209C,FALSE,FALSE,TRUE,FALSE
-YDR222W,FALSE,FALSE,TRUE,FALSE
-YDR364C,FALSE,FALSE,TRUE,FALSE
-YDR370C,FALSE,FALSE,TRUE,FALSE
-YDR459C,FALSE,FALSE,TRUE,FALSE
-YDR468C,FALSE,FALSE,TRUE,FALSE
-YDR473C,FALSE,FALSE,TRUE,FALSE
-YDR540C,FALSE,FALSE,TRUE,FALSE
-YEL021W,FALSE,FALSE,TRUE,FALSE
-YER037W,FALSE,FALSE,TRUE,FALSE
-YER045C,FALSE,FALSE,TRUE,FALSE
-YER132C,FALSE,FALSE,TRUE,FALSE
-YER149C,FALSE,FALSE,TRUE,FALSE
-YFL007W,FALSE,FALSE,TRUE,FALSE
-YFR026C,FALSE,FALSE,TRUE,FALSE
-YFR027W,FALSE,FALSE,TRUE,FALSE
-YGL044C,FALSE,FALSE,TRUE,FALSE
-YGL164C,FALSE,FALSE,TRUE,FALSE
-YGL196W,FALSE,FALSE,TRUE,FALSE
-YGL224C,FALSE,FALSE,TRUE,FALSE
-YGR108W,FALSE,FALSE,TRUE,FALSE
-YHR067W,FALSE,FALSE,TRUE,FALSE
-YHR139C,FALSE,FALSE,TRUE,FALSE
-YHR158C,FALSE,FALSE,TRUE,FALSE
-YHR172W,FALSE,FALSE,TRUE,FALSE
-YIL001W,FALSE,FALSE,TRUE,FALSE
-YIL119C,FALSE,FALSE,TRUE,FALSE
-YIL135C,FALSE,FALSE,TRUE,FALSE
-YIR020C,FALSE,FALSE,TRUE,FALSE
-YJL016W,FALSE,FALSE,TRUE,FALSE
-YJL024C,FALSE,FALSE,TRUE,FALSE
-YJL049W,FALSE,FALSE,TRUE,FALSE
-YJL091C,FALSE,FALSE,TRUE,FALSE
-YJL094C,FALSE,FALSE,TRUE,FALSE
-YJL126W,FALSE,FALSE,TRUE,FALSE
-YJL147C,FALSE,FALSE,TRUE,FALSE
-YJL156C,FALSE,FALSE,TRUE,FALSE
-YJR010C-A,FALSE,FALSE,TRUE,FALSE
-YJR022W,FALSE,FALSE,TRUE,FALSE
-YJR046W,FALSE,FALSE,TRUE,FALSE
-YJR054W,FALSE,FALSE,TRUE,FALSE
-YJR155W,FALSE,FALSE,TRUE,FALSE
-YKL021C,FALSE,FALSE,TRUE,FALSE
-YKL031W,FALSE,FALSE,TRUE,FALSE
-YKL075C,FALSE,FALSE,TRUE,FALSE
-YKL076C,FALSE,FALSE,TRUE,FALSE
-YKL111C,FALSE,FALSE,TRUE,FALSE
-YKL114C,FALSE,FALSE,TRUE,FALSE
-YKL116C,FALSE,FALSE,TRUE,FALSE
-YKL132C,FALSE,FALSE,TRUE,FALSE
-YKL173W,FALSE,FALSE,TRUE,FALSE
-YKL201C,FALSE,FALSE,TRUE,FALSE
-YKR023W,FALSE,FALSE,TRUE,FALSE
-YKR028W,FALSE,FALSE,TRUE,FALSE
-YKR035C,FALSE,FALSE,TRUE,FALSE
-YKR050W,FALSE,FALSE,TRUE,FALSE
-YKR060W,FALSE,FALSE,TRUE,FALSE
-YKR063C,FALSE,FALSE,TRUE,FALSE
-YKR086W,FALSE,FALSE,TRUE,FALSE
-YKR104W,FALSE,FALSE,TRUE,FALSE
-YLL052C,FALSE,FALSE,TRUE,FALSE
-YLL053C,FALSE,FALSE,TRUE,FALSE
-YLL067C,FALSE,FALSE,TRUE,FALSE
-YLR022C,FALSE,FALSE,TRUE,FALSE
-YLR051C,FALSE,FALSE,TRUE,FALSE
-YLR098C,FALSE,FALSE,TRUE,FALSE
-YLR119W,FALSE,FALSE,TRUE,FALSE
-YLR211C,FALSE,FALSE,TRUE,FALSE
-YLR214W,FALSE,FALSE,TRUE,FALSE
-YLR226W,FALSE,FALSE,TRUE,FALSE
-YLR227C,FALSE,FALSE,TRUE,FALSE
-YLR246W,FALSE,FALSE,TRUE,FALSE
-YLR297W,FALSE,FALSE,TRUE,FALSE
-YLR306W,FALSE,FALSE,TRUE,FALSE
-YLR319C,FALSE,FALSE,TRUE,FALSE
-YLR323C,FALSE,FALSE,TRUE,FALSE
-YLR361C,FALSE,FALSE,TRUE,FALSE
-YLR376C,FALSE,FALSE,TRUE,FALSE
-YLR403W,FALSE,FALSE,TRUE,FALSE
-YLR404W,FALSE,FALSE,TRUE,FALSE
-YLR410W,FALSE,FALSE,TRUE,FALSE
-YLR424W,FALSE,FALSE,TRUE,FALSE
-YML034W,FALSE,FALSE,TRUE,FALSE
-YMR014W,FALSE,FALSE,TRUE,FALSE
-YMR021C,FALSE,FALSE,TRUE,FALSE
-YMR047C,FALSE,FALSE,TRUE,FALSE
-YMR077C,FALSE,FALSE,TRUE,FALSE
-YMR080C,FALSE,FALSE,TRUE,FALSE
-YMR169C,FALSE,FALSE,TRUE,FALSE
-YMR223W,FALSE,FALSE,TRUE,FALSE
-YMR255W,FALSE,FALSE,TRUE,FALSE
-YMR262W,FALSE,FALSE,TRUE,FALSE
-YMR288W,FALSE,FALSE,TRUE,FALSE
-YMR306W,FALSE,FALSE,TRUE,FALSE
-YMR320W,FALSE,FALSE,TRUE,FALSE
-YNL042W,FALSE,FALSE,TRUE,FALSE
-YNL050C,FALSE,FALSE,TRUE,FALSE
-YNL108C,FALSE,FALSE,TRUE,FALSE
-YNL158W,FALSE,FALSE,TRUE,FALSE
-YNL218W,FALSE,FALSE,TRUE,FALSE
-YNL231C,FALSE,FALSE,TRUE,FALSE
-YNL238W,FALSE,FALSE,TRUE,FALSE
-YNL279W,FALSE,FALSE,TRUE,FALSE
-YNL282W,FALSE,FALSE,TRUE,FALSE
-YNR039C,FALSE,FALSE,TRUE,FALSE
-YNR044W,FALSE,FALSE,TRUE,FALSE
-YNR051C,FALSE,FALSE,TRUE,FALSE
-YNR057C,FALSE,FALSE,TRUE,FALSE
-YNR075W,FALSE,FALSE,TRUE,FALSE
-YOL070C,FALSE,FALSE,TRUE,FALSE
-YOL105C,FALSE,FALSE,TRUE,FALSE
-YOL137W,FALSE,FALSE,TRUE,FALSE
-YOL151W,FALSE,FALSE,TRUE,FALSE
-YOL154W,FALSE,FALSE,TRUE,FALSE
-YOL164W,FALSE,FALSE,TRUE,FALSE
-YOR028C,FALSE,FALSE,TRUE,FALSE
-YOR051C,FALSE,FALSE,TRUE,FALSE
-YOR059C,FALSE,FALSE,TRUE,FALSE
-YOR062C,FALSE,FALSE,TRUE,FALSE
-YOR130C,FALSE,FALSE,TRUE,FALSE
-YOR161C,FALSE,FALSE,TRUE,FALSE
-YOR192C,FALSE,FALSE,TRUE,FALSE
-YOR194C,FALSE,FALSE,TRUE,FALSE
-YOR328W,FALSE,FALSE,TRUE,FALSE
-YOR390W,FALSE,FALSE,TRUE,FALSE
-YPL159C,FALSE,FALSE,TRUE,FALSE
-YPL162C,FALSE,FALSE,TRUE,FALSE
-YPL233W,FALSE,FALSE,TRUE,FALSE
-YPR003C,FALSE,FALSE,TRUE,FALSE
-YPR046W,FALSE,FALSE,TRUE,FALSE
-YPR053C,FALSE,FALSE,TRUE,FALSE
-YPR066W,FALSE,FALSE,TRUE,FALSE
-YPR084W,FALSE,FALSE,TRUE,FALSE
-YPR101W,FALSE,FALSE,TRUE,FALSE
-YPR119W,FALSE,FALSE,TRUE,FALSE
-YPR149W,FALSE,FALSE,TRUE,FALSE
-YPR152C,FALSE,FALSE,TRUE,FALSE
-YPR157W,FALSE,FALSE,TRUE,FALSE
-YPR158W,FALSE,FALSE,TRUE,FALSE
-YAR075W,FALSE,FALSE,FALSE,TRUE
-YBR031W,FALSE,FALSE,FALSE,TRUE
-YDL130W,FALSE,FALSE,FALSE,TRUE
-YDL174C,FALSE,FALSE,FALSE,TRUE
-YDL181W,FALSE,FALSE,FALSE,TRUE
-YDR178W,FALSE,FALSE,FALSE,TRUE
-YDR342C,FALSE,FALSE,FALSE,TRUE
-YDR529C,FALSE,FALSE,FALSE,TRUE
-YEL024W,FALSE,FALSE,FALSE,TRUE
-YFR033C,FALSE,FALSE,FALSE,TRUE
-YGL147C,FALSE,FALSE,FALSE,TRUE
-YGL162W,FALSE,FALSE,FALSE,TRUE
-YGL187C,FALSE,FALSE,FALSE,TRUE
-YGL191W,FALSE,FALSE,FALSE,TRUE
-YGR027C,FALSE,FALSE,FALSE,TRUE
-YHR001W,FALSE,FALSE,FALSE,TRUE
-YHR005C,FALSE,FALSE,FALSE,TRUE
-YHR051W,FALSE,FALSE,FALSE,TRUE
-YHR216W,FALSE,FALSE,FALSE,TRUE
-YIL070C,FALSE,FALSE,FALSE,TRUE
-YJR048W,FALSE,FALSE,FALSE,TRUE
-YJR158W,FALSE,FALSE,FALSE,TRUE
-YKL148C,FALSE,FALSE,FALSE,TRUE
-YLL041C,FALSE,FALSE,FALSE,TRUE
-YLR038C,FALSE,FALSE,FALSE,TRUE
-YLR089C,FALSE,FALSE,FALSE,TRUE
-YLR395C,FALSE,FALSE,FALSE,TRUE
-YMR145C,FALSE,FALSE,FALSE,TRUE
-YNL052W,FALSE,FALSE,FALSE,TRUE
-YOR293W,FALSE,FALSE,FALSE,TRUE
-YPL078C,FALSE,FALSE,FALSE,TRUE
-YPL271W,FALSE,FALSE,FALSE,TRUE
-YPR020W,FALSE,FALSE,FALSE,TRUE
-YPR191W,FALSE,FALSE,FALSE,TRUE
Deleted: pkg/CHNOSZ/inst/extdata/abundance/yeastgfp.csv.xz
===================================================================
(Binary files differ)
Deleted: pkg/CHNOSZ/inst/extdata/protein/Sce.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/inst/extdata/thermo/protein.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/protein.csv 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/inst/extdata/thermo/protein.csv 2019-10-19 06:22:14 UTC (rev 508)
@@ -505,3 +505,8 @@
HXD11,HUMAN,UniProt,P31277,1,48,6,11,19,16,50,2,4,16,16,6,10,41,15,21,23,7,10,2,15
HXD12,HUMAN,UniProt,P35452,1,39,4,7,13,10,24,0,4,16,28,3,11,28,15,19,17,10,9,3,10
HXD13,HUMAN,UniProt,P35453,1,54,5,11,13,11,32,7,7,18,14,7,11,23,13,19,45,12,20,5,16
+YDL195W,Sce,S000002354,SEC31,1,107,7,59,75,43,53,22,60,82,110,20,100,111,57,27,141,94,61,19,25
+YHR098C,Sce,S000001140,SFB3,1,43,18,58,36,40,47,21,59,47,94,23,59,49,52,33,87,58,63,2,40
+YLR208W,Sce,S000004198,SEC13,1,23,3,17,23,5,22,12,16,20,24,1,13,10,7,8,26,18,27,15,7
+YNL049C,Sce,S000004994,SFB2,1,45,13,54,55,38,35,14,55,39,96,22,55,52,37,45,79,50,55,3,34
+YPL085W,Sce,S000006006,SEC16,1,141,3,135,158,59,95,48,116,162,155,34,168,175,113,58,249,141,115,16,54
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2019-10-19 06:22:14 UTC (rev 508)
@@ -24,7 +24,7 @@
\item Thermodynamic data: \code{\link{data}}, \code{\link{extdata}}, \code{\link{add.obigt}}, \code{\link{util.data}}
\item Thermodynamic calculations: \code{\link{util.formula}}, \code{\link{makeup}}, \code{\link{util.units}}, \code{\link{eos}}, \code{\link{berman}}, \code{\link{nonideal}}, \code{\link{util.misc}}
\item Water properties: \code{\link{water}}, \code{\link{util.water}}, \code{\link{DEW}}, \code{\link{IAPWS95}}
- \item Protein properties: \code{\link{protein}}, \code{\link{protein.info}}, \code{\link{add.protein}}, \code{\link{util.fasta}}, \code{\link{util.protein}}, \code{\link{util.seq}}, \code{\link{ionize.aa}}, \code{\link{yeast}}
+ \item Protein properties: \code{\link{protein}}, \code{\link{protein.info}}, \code{\link{add.protein}}, \code{\link{util.fasta}}, \code{\link{util.protein}}, \code{\link{util.seq}}, \code{\link{ionize.aa}}
\item Other tools: \code{\link{examples}}, \code{\link{eqdata}}, \code{\link{taxonomy}}, \code{\link{util.blast}}
\item Utility functions: \code{\link{util.expression}}, \code{\link{util.plot}}, \code{\link{util.array}}, \code{\link{util.matrix}}, \code{\link{util.list}}, \code{\link{util.test}}, \code{\link{palply}}
}
Modified: pkg/CHNOSZ/man/add.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/add.protein.Rd 2019-09-10 04:31:33 UTC (rev 507)
+++ pkg/CHNOSZ/man/add.protein.Rd 2019-10-19 06:22:14 UTC (rev 508)
@@ -59,7 +59,7 @@
}
\seealso{
-\code{\link{read.fasta}}, \code{\link{uniprot.aa}}, \code{\link{yeast.aa}} for other ways of getting amino acid compositions.
+\code{\link{read.fasta}} and \code{\link{uniprot.aa}} for other ways of getting amino acid compositions.
\code{\link{pinfo}} for protein-level functions (length, chemical formulas, reaction coefficients of basis species).
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 508
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