[GenABEL-dev] [Fwd: descriptives.trait Patch]
pirastu at burlo.trieste.it
pirastu at burlo.trieste.it
Fri Mar 25 13:03:57 CET 2011
Sorry I forgot the attachment.
Dear all,
attached you can find a patch to fix the bugs described underneath. To
install from the root directory of /pkg: patch -p0 <
patch_descriptives.trait.
Best
Nicola
Patch for bugs #1184 #1185 #1259
Bug [#1184] descriptives.trait can not see the variable in by.var argument
unless full path specified
Description:
https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1184&group_id=505&atid=2058
Changes: now by.var can be specified aslo as :"var_name" or ~var_name
Test:
> library(GenABEL)
> data(ge03d2ex)
> descriptives.trait(ge03d2ex,by.var="sex")
No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw
id 64 NA NA 72 NA NA NA NA
sex 64 NA NA 72 NA NA NA NA
age 64 46.942 12.479 72 50.959 13.107 0.070 0.081
dm2 64 0.547 0.502 72 0.708 0.458 0.053 0.052
height 64 162.680 6.819 71 175.534 7.943 0.000 0.000
weight 64 78.605 26.908 71 95.322 21.441 0.000 0.000
diet 64 0.109 0.315 72 0.014 0.118 0.025 0.019
bmi 64 29.604 9.506 71 30.930 6.547 0.352 0.040
Pexact
id NA
sex NA
age NA
dm2 0.074
height NA
weight NA
diet 0.026
bmi NA
> descriptives.trait(ge03d2ex,by.var=~sex)
No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw
id 64 NA NA 72 NA NA NA NA
sex 64 NA NA 72 NA NA NA NA
age 64 46.942 12.479 72 50.959 13.107 0.070 0.081
dm2 64 0.547 0.502 72 0.708 0.458 0.053 0.052
height 64 162.680 6.819 71 175.534 7.943 0.000 0.000
weight 64 78.605 26.908 71 95.322 21.441 0.000 0.000
diet 64 0.109 0.315 72 0.014 0.118 0.025 0.019
bmi 64 29.604 9.506 71 30.930 6.547 0.352 0.040
Pexact
id NA
sex NA
age NA
dm2 0.074
height NA
weight NA
diet 0.026
bmi NA
Bug [#1185] descriptives.trait with missings in by.var argument
Description:
https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1185&group_id=505&atid=2058
Fixed: now by.var argument acceptes missing
Test:
> phdata(ge03d2ex)$sex[2] <- NA
> descriptives.trait(ge03d2ex,by.var=phdata(ge03d2ex)$sex)
No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw
id 63 NA NA 72 NA NA NA NA
sex 63 NA NA 72 NA NA NA NA
age 63 47.003 12.570 72 50.959 13.107 0.076 0.088
dm2 63 0.540 0.502 72 0.708 0.458 0.045 0.044
height 63 162.573 6.819 71 175.534 7.943 0.000 0.000
weight 63 77.651 26.009 71 95.322 21.441 0.000 0.000
diet 63 0.111 0.317 72 0.014 0.118 0.024 0.017
bmi 63 29.306 9.277 71 30.930 6.547 0.250 0.025
Pexact
id NA
sex NA
age NA
dm2 0.051
height NA
weight NA
diet 0.025
bmi NA
Bug [#1259] descriptives.trait with by.var argument does not work
(contributed by Richard Ahn)
Description:
https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1259&group_id=505&atid=2058
Comments: The problem was that for one of the traits one of the categories
had all missing data, this made descriptives.trait crush.
Fixed: descriptives.trait does not crush anymore.
Test:
nicola at nicola-VirtualBox:~/Scrivania$ R -f test.R
WARNING: ignoring environment value of R_HOME
R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R è un software libero ed è rilasciato SENZA ALCUNA GARANZIA.
Siamo ben lieti se potrai redistribuirlo, ma sotto certe condizioni.
Scrivi 'license()' o 'licence()' per dettagli su come distribuirlo.
R è un progetto di collaborazione con molti contributi esterni.
Scrivi 'contributors()' per maggiori informazioni e 'citation()'
per sapere come citare R o i pacchetti di R nelle pubblicazioni.
Scrivi 'demo()' per una dimostrazione, 'help()' per la guida in linea, o
'help.start()' per l'help navigabile con browser HTML.
Scrivi 'q()' per uscire da R.
> library(GenABEL)
Carico il pacchetto richiesto: MASS
GenABEL v. 1.6-6 (February 24, 2011) loaded
Installed GenABEL version (1.6-6) is not the same as stable
version available from CRAN (1.6-5). Unless used intentionally,
consider updating to the latest CRAN version. For that, use
'install.packages("GenABEL")', or ask your system administrator
to update the package.
> convert.snp.illumina(infile="test_markers", outfile="test.raw")
Reading genotypes from file 'test_markers' ...
Writing to file 'test.raw' ...
... done.
> test = load.gwaa.data(pheno="test_phenos", geno="test.raw", force=T)
ids loaded...
marker names loaded...
chromosome data loaded...
map data loaded...
allele coding data loaded...
strand data loaded...
genotype data loaded...
snp.data object created...
assignment of gwaa.data object FORCED; X-errors were not checked!
> attach(phdata(test))
> descriptives.trait(data=test, by = bt)
Error in t.test.formula(ctrao ~ svar) :
grouping factor must have exactly 2 levels
Error in kruskal.test.default(c(6L, 32L, 35L, 33L, 52L, 25L), c(1L, 1L, :
all observations are in the same group
No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw Pexact
id 5 NA NA 6 NA NA NA NA NA
sex 5 0.2 0.447 6 0.333 0.516 0.657 0.637 1
age 0 NaN NA 6 30.500 14.977 NA NA NA
bt 5 NA NA 6 NA NA NA NA NA
>
>
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