splitNrenameSamples: Rename samples from array codes to user codes, and split...

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Rename samples from array codes to user codes, and split diploid from polyploid samples

Description

After conversion of array data to fitPoly format, this function replaces the array codes for the samples to user codes, and it splits the data into a part for diploid and one for polyploid samples if both are present.

Usage

splitNrenameSamples(dat, sampletable, SampleID, CustomerID,
Ploidy=NULL, out, filetype=c("dat","RData")[2])

Arguments

dat	a data frame in "long" format as returned by readFullDataTable or readAxiomSummary
sampletable	a data frame with at least the columns for SampleID, CustomerID and Ploidy (these columns may have any name, specified by the next parameters)
SampleID	the title of the column in sampletable containing the codes for the samples in the array file - there must be a one-to-one relation between the array codes and the user codes!
CustomerID	the title of the column in sampletable containing the user codes for the samples - there must be a one-to-one relation between the array codes and the user codes!
Ploidy	the title of the column in sampletable containing the ploidy of the samples; default NULL means no split based on ploidy must be done. If not NULL, for each different ploidy a separate data.frame will be created and samples with ploidy missing or "" will be omitted from all files.
out	the base filename of the output files; to this will be appended the the ploidy level(s) if Ploidy is not NULL, and an extension .dat or .RData, depending on filetype). Setting out to NA or "" results in no output file(s) being created
filetype	either "dat" or "RData" (default): the former produces tab- separated text files (one for each element of the return value), the latter saves one RData file containing a list named dat, identical to the return value

Value

if Ploidy not specified, the original dat data.frame with substituted SampleNames; if Ploidy specified a list with one element for each different value in the Ploidy column; the names of the elements are then these ploidy values. Each element is a subset of the original dat data.frame containing only the rows with samples of that ploidy, and with substituted SampleNames

fitPoly documentation built on April 3, 2025, 8:58 p.m.