consensusRank: Consensus Ranking of Genes

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Consensus Ranking of Genes

Description

Calculate the consensus ordering for genes from a set of transcripts or differential expression (DE) files

Usage

consensusRank(  fileSet, fids = basename(fileSet), 
		colorSet = 2:(length(fileSet) + 1), 
		geneColumn = "GENE_ID", 
		valueColumn = "LOG_2_FOLD", speciesID = getCurrentSpecies(),
		keepNonGenes = FALSE, weights = 1, altGeneMap = NULL, 
		annotationColumns = "PRODUCT", label = "", cex = 1, useLog = FALSE)

Arguments

fileSet	characer vector of explicit filenames of transcripts or DE results
fids	sample IDs for each file
colorSet	colors for each file
geneColumn	the column name for the GeneIDs
valueColumn	the column name for the expression or DE value to use
speciesID	speciesID for these files
keepNonGenes	logical, should all rows or just real genes be used
weights	the relative weight to give to each file
altGeneMap	alternative GeneMap to use instead of the current MapSet
annotationColumns	characer vector of extra columns to carry forward from the current GeneMap to the output result
label	optional text for the plot heading
cex	plot point expansion factor
useLog	logical, should the Y axis be drawn in log scale

Details

Calculate the consensus from a family of result files, either transcriptomes or DE fold change results. Measures the average rank and value (expression or fold change) for every gene, and creates a new result that represents the (weighted) average of the given files.

Value

a data frame of the genes in common to all files, sorted by rank and value. The first 2 elements are the genes and values, with column names geneColumn and valueColumn.

The third column is the average RANK, by square-root mean as in metaRank

Lastly, any other columns from annotationColumns are carried forward from the GeneMap.

Note

Only genes in common to ALL input files are used, thus the output data frame may have less rows then the input files.

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.