readAxiomSummary: convert an Affymetrix AxiomCT1.summary file to the import...

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

convert an Affymetrix AxiomCT1.summary file to the import format for fitPoly

Description

An Affymetrix AxiomCT1.summary.txt file in wide format (samples side-by-side) is converted to a fitPoly input file in long format

Usage

readAxiomSummary(AXdata, markergroups=list(),
out, filetype=c("dat", "RData")[2])

Arguments

AXdata	name of an AxiomCT1.summary.txt tab-separated text file exported from Affymetrix Power Tools (APT); or a data.frame in the same format: the file may start with a number of comment lines (starting with "#") followed by a header line of which the first caption is "probeset_id" and all other captions are sample names, all ending with ".CEL". For each marker there are two lines, with probeset_id ending in "-A" and "-B"; the two lines for each marker are consecutive. In addition there may be any number of control markers, for each of which there is only one line, with probeset_id ending in "-A".
markergroups	a list with character vectors of marker names, or integer vectors of marker numbers in file order. If the data set is large, the conversion to long format may exceed memory limits. In these cases the data can be split into marker groups that are converted separately and each saved to a file (or returned as list items, but if that is possible splitting into groups would not be needed)
out	the name of an output file (without extension). If a list of markergroups is given, out must be a valid file name (without extension); in that case multiple output files are created with filenames in which the list element numbers are appended to out. If no markergroups are specified out may also be set to "" or NA; in that case no file is created and the converted data are only returned as function result. If out is not "" or NA, then also a file <out>_meanR.dat is saved with for all samples their mean R value and number of missing data (over all markers)
filetype	either "dat" or "RData" (default): the former produces tab-separated text files, the latter saves RData files with the converted data in a data frame with name "dat"

Details

The wide-format input is converted to a long-format form with columns MarkerName, SampleName, X, Y, R (= X + Y) and ratio (= Y / R). The X and Y signal intensities are obtained from the <marker>-A and <marker>-B rows in the input data, R and ratio are calculated from these values.

Value

If no markergroups are specified, a data.frame is returned with columns MarkerName, SampleName, X, Y, R (= X + Y), ratio (= Y / (X+Y) ).
If a list of markergroups is specified the function result is NULL and the converted data.frames are only saved as files.
If the saved files are RData files, they all contain one data.frame named "dat".

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