convert.gct2submap: Prepare data for use in SubMap.

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

Converts a gct file and cls file so that:
- one row per gene symbol & gene symbol becomes the Name of each row, rather than the probe id
– different methods of collapsing rows
- cls file starts from 1, rather than 0
- choose the most variable genes, either by a coefficient of variation threshold (eg 50)
or the top N most variable genes, as defined by CV.

Usage

convert.gct2submap(gct.file, cls.file, chip.file, gct.out, cls.out,
  collapse.mode = c("max.avg", "mean", "median", "max.cv"),
  cv.thresh = NULL, topN.thresh = NULL)

Arguments

gct.file	standard input files to be modified.
cls.file	standard input files to be modified.
chip.file	used to map probe ID's to gene symbols
gct.out	output files.
cls.out	output files.
collapse.mode	how to choose the value for each gene.
cv.thresh	[optional] CV threshold to use. CV's are percentages, so 50, or 100 is a good place to start. Thresholding is done after collapsing to unique genes. This overrides topN.thresh.
topN.thresh	[optional] take the top N genes when ranked by their CV's. Must leave cv.thresh=NULL. Thresholding is done after collapsing to unique genes.
max.avg	calculate the average for each probeset & choose the values from the probes with largest average value
mean	for N probesets mapping to the same gene, calculate the mean or median of those N values for each sample.
median	for N probesets mapping to the same gene, calculate the mean or median of those N values for each sample.
max.cv	calculate the CV for each probe & choose the values from the probe with highest cv

Value

creates a new gct & cls file. The gct file has 1 row per gene which passed the filters & has gene symbols in column 1 (the Name column). The cls file starts from '1' instead of '0' which means it may not work with other GenePattern modules!

Author(s)

Mark Cowley, 2010-07-06

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.