[Rcolony-commits] r46 - pkg/man

Fri May 8 11:16:20 CEST 2009

Author: jonesor
Date: 2009-05-08 11:16:20 +0200 (Fri, 08 May 2009)
New Revision: 46

Modified:
   pkg/man/build.colony.input.Rd
Log:
Converted build.colony.input.Rd to ASCII following reported build errors

Modified: pkg/man/build.colony.input.Rd
===================================================================

--- pkg/man/build.colony.input.Rd	2009-05-08 09:11:34 UTC (rev 45)
+++ pkg/man/build.colony.input.Rd	2009-05-08 09:16:20 UTC (rev 46)
@@ -7,11 +7,8 @@
 This function prompts the user to provide information about their system in order to correctly build and format a Colony2 input file.
 }
 
-\usage{
-build.colony.input(wd=getwd(),name="Colony2.DAT")
+\usage{build.colony.input(wd=getwd(),name="Colony2.DAT")}
 
-}
-
 \arguments{
   \item{wd}{The directory where the generated file will be placed. The default is the current working directory.}
   \item{name}{The desired filename for the Colony input file (the default is Colony2.DAT).}
@@ -95,7 +92,7 @@
 
 \emph{Select the marker type and error rate file.}	You will be prompted to select the file for the markers. In the file, 4 values are provided for each marker (in columns). The first value (on row 1) specifies the marker name or ID (consisting of a maximum of  20 letters/numbers, others such as space, comma, full stop, forward and backward slashes are not allowed in the name/ID). The second (on row 2) indicates the marker type, whether it is codominant (0) or dominant (1). The third and fourth values (on rows 3 and 4 respectively) give the allelic dropout rate and the rate of other kinds of genotyping errors (including mutations) of the marker. For more information about the models of genotyping errors, see \cite{Wang (2004)}.
 
-Note that this file sets the order of marker loci that must be followed in all the following input. The first column is for locus 1, the second for locus 2, É
+Note that this file sets the order of marker loci that must be followed in all the following input. The first column is for locus 1, the second for locus 2, etc.
 
 Note also that computation becomes slow when markers suffer from genotyping errors. This is especially obvious when both males and females are specified as polygamous.
 
@@ -106,11 +103,8 @@
        0 \tab       0 \tab      0 \tab      0 \tab       0 \cr
   0.0000 \tab  0.0000 \tab 0.0000 \tab 0.0000 \tab  0.0000 \cr
   0.0001 \tab  0.0001 \tab  0.0001 \tab 0.0001 \tab  0.0001 \cr
-
 }
 
-
-
 \emph{Offspring genotypes.}
 
 You will be prompted to select the offspring genotype file. The file contains the individual IDs and the genotypes at each locus. Each individual takes a single row. The first column gives the individual ID (a string containing a maximum of 20 letters and/or numbers, no other characters are allowed), the 2nd and 3rd columns give the alleles observed for the individual at the first locus, the 4th and 5th give the alleles observed for the individual at the 2nd locus, etc. An allele is identified by an integer, in the range of 1-999999999. If the locus is a dominant marker, then only one (instead of 2) column is required for the marker, and the value for the genotype should be either 1 (dominant phenotype, presence of a band) or 2 (recessive phenotype, absence of a band). Missing genotypes are indicated by 0  0  for a codominant marker and 0 for a dominant marker. Note that offspring IDs should be unique. They are case sensitive, which means that, for example, "offspring2" and "Offspring2" are treated as different. An offspring with missing genotypes at all loci (no marker information at all) should not be included in the offspring genotype file.
@@ -152,12 +146,10 @@
 
 \emph{Select the maternal diads file.} If the number of known maternal diads is larger than zero, then you will be prompted to select a file for the known maternal diads. This file should have 2 columns, the first gives mother ID, while the second gives the corresponding offspring ID.
 
-
 \emph{Number of known paternal sibships.} Provide the number of known paternal sibship or paternity included in the samples. The minimum value is 0. A known paternal sibship contains all of the offspring in the OFS sample who are known to share the same father no matter whether the father is known or not.
 
 \emph{Select the paternal sibships file.} If the number of known paternal sibship/paternity is larger than zero, then you will be prompted to select a file for the known paternal sibship/paternity. In the file, each known paternal sibship/paternity takes a row, with the first column containing the father ID/name if the male is known and included in the candidate males or a value of 0 to indicate that the father is unknown or not in the candidate males. From the 2nd column on, the ID/name of each member of the paternal sibship is listed.
 
-
 \emph{Number of known maternal sibships.} Provide the number of known maternal sibship or maternity included in the samples. The minimum value is 0. A known maternal sibship contains all of the offspring in the OFS sample who are known to share the same mother no matter whether the mother is known or not.
 
 \emph{Select the maternal sibships file.} If the number of known maternal sibship/maternity is larger than zero, then you will be prompted to select a file for the known maternal sibship/maternity. In the file, each known maternal sibship/maternity takes a row, with the first column containing the mother ID/name if the male is known and included in the candidate females or a value of 0 to indicate that the mother is unknown or not in the candidate females. From the 2nd column on, the ID/name of each member of the maternal sibship is listed.

