Convert Genotype Data
GenoConvert.Rd
Convert genotype data in various formats to sequoia's 1-column-per-marker format or Colony's 2-columns-per-marker format.
Arguments
- InData
dataframe or matrix with genotypes to be converted.
- InFile
character string with name of genotype file to be converted.
- InFormat
One of 'single', 'double', 'col', 'ped', 'raw', or 'seq', see Details.
- OutFile
character string with name of converted file. If NA, return matrix with genotypes in console (default); if NULL, write to 'GenoForSequoia.txt' in current working directory.
- OutFormat
as
InFormat
; only 'seq', 'col', and 'ped' are implemented. For 'ped' also a sham .map file is created, so that the file can be read by PLINK. Only for 'ped' are extensions .ped & .map added to the specified OutFile filename.- Missing
vector with symbols interpreted as missing data. '0' is missing data for InFormats 'col' and 'ped' only.
- sep
vector with field separator strings that will be tried on
InFile
. TheOutFile
separator uses thewrite.table
default, i.e. one blank space.- header
a logical value indicating whether the file contains a header as its first line. If NA (default), set to TRUE for 'raw', and FALSE otherwise.
- IDcol
number giving the column with individual IDs; 0 indicates the rownames (for InData only). If NA (default), set to 2 for InFormat 'raw' and 'ped', and otherwise to 1 for InFile and 0 (rownames) for InData, except when InData has a column labeled 'ID'.
- FIDcol
column with the family IDs, if any are wished to be used. This is column 1 for InFormat 'raw' and 'seq', but those are by default not used.
- FIDsep
string used to paste FID and IID together into a composite-ID (value passed to
paste
'scollapse
). This joining can be reversed usingPedStripFID
.- dropcol
columns to exclude from the output data, on top of IDcol and FIDcol (which become rownames). When NA, defaults to columns 3-6 for InFormat 'raw' and 'seq'. Can also be used to drop some SNPs, see example below on how to do this for the 2-columns-per-SNP input formats.
- quiet
suppress messages and warnings.
Value
A genotype matrix in the specified output format. If 'OutFile' is specified, the matrix is written to this file and nothing is returned inside R. When converting to 0/1/2 format, 2 is the homozygote for the minor allele, and 0 the homozygote for the major allele.
Details
The first two arguments are interchangeable, and can be given unnamed. The first argument is assumed to be a file name if it is of class 'character' and length 1, and to be the genetic data if it is a matrix or dataframe.
Input formats
The following formats can be specified by InFormat
:
- seq
(sequoia) genotypes are coded as 0, 1, 2, missing as \(-9\), in 1 column per marker. Column 1 contains IDs, there is no header row.
- raw
(PLINK) genotypes are coded as 0, 1, 2, missing as NA, in 1 column per marker. The first 6 columns are descriptive (1:FID, 2:IID, 3 to 6 ignored), and there is a header row. This is produced by PLINK's option --recodeA
- ped
(PLINK) genotypes are coded as A, C, T, G, missing as 0, in 2 columns per marker. The first 6 columns are descriptive (1:FID, 2:IID, 3 to 6 ignored).
- col
(Colony) genotypes are coded as numeric values, missing as 0, in 2 columns per marker. Column 1 contains IDs.
- single
1 column per marker, otherwise unspecified
- double
2 columns per marker, otherwise unspecified
For each InFormat
, its default values for Missing, header,
IDcol, FIDcol
, and dropcol
can be overruled by specifying the
corresponding input parameters.
Error messages
Occasionally when reading in a file GenoConvert
may give an error
that 'rows have unequal length'. GenoConvert makes use of
readLines
and strsplit
, which is much faster
than read.table
for large datafiles, but also more sensitive
to unusual line endings, unusual end-of-file characters, or invisible
characters (spaces or tabs) after the end of some lines. In these cases,
try to read the data from file using read.table or read.csv, and then use
GenoConvert
on this dataframe or matrix, see example.
Author
Jisca Huisman, jisca.huisman@gmail.com
Examples
if (FALSE) {
# Requires PLINK installed & in system PATH:
# tinker with window size, window overlap and VIF to get a set of
# 400 - 800 markers (100-200 enough for just parentage):
system("cmd", input = "plink --file mydata --indep 50 5 2")
system("cmd", input = "plink --file mydata --extract plink.prune.in
--recodeA --out PlinkOUT")
GenoM <- GenoConvert(InFile = "PlinkOUT.raw")
# save time on file conversion next time:
write.table(GenoM, file="Geno_sequoia.txt", quote=FALSE, col.names=FALSE)
GenoM <- as.matrix(read.table("Geno_sequoia.txt", row.names=1, header=FALSE))
# drop some SNPs, e.g. after a warning of >2 alleles:
dropSNP <- c(5,68,101,128)
GenoM <- GenoConvert(ColonyFile, InFormat = "col",
dropcol = 1 + c(2*dropSNP-1, 2*dropSNP) )
# circumvent a 'rows have unequal length' error:
GenoTmp <- as.matrix(read.table("mydata.txt", header=TRUE, row.names=1))
GenoM <- GenoConvert(InData=GenoTmp, InFormat="single", IDcol=0)
}