consensusRank: Consensus Ranking of Genes

Description Usage Arguments Details Value Note

Description

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

Usage

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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 Dec. 7, 2018, 8:02 a.m.