significantGenes: Select Significant Genes from a Differential Expression...

Description Usage Arguments Value Note Author(s)

Description

Select the subset of genes that meet both minimum fold change and maximum P-value criteria, from a file that wwas produced by a Differential Expression tool.

Usage

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significantGenes(file, geneColumn = "GENE_ID", foldColumn = "LOG2FOLD", pvalueColumn = "PVALUE", 
		keepIntergenics = FALSE, min.fold = 1, max.pvalue = 0.05, min.genes = NULL, 
		shortNames = TRUE, sep = "\t", verbose = TRUE)

Arguments

file

character string of one full path filename.

geneColumn

character string of one column name, that contains the GeneIDs.

foldColumn

character string of one column name, that contains the fold change values.

pvalueColumn

character string of one column name, that contains the significance values.

keepIntergenics

logical, should non-genes be excluded from consideration.

min.fold

numeric value for the inclusion cutoff based on fold change.

max.pvalue

numeric value for the inclusion cutoff based on significance.

min.genes

optional numeric value, giving the minimum number of genes to return.

shortNames

logical, should the returned GeneIDs be shortened to their gene symbol only.

sep

file field separator, passed to read.table.

Value

A data frame of significant genes:

GENE_ID

the identifiers of the significant genes

PRODUCT

their gene product terms

LOG2FOLD

their fold change values

PVALUE

their significance values

Note

This function is intended to be generic with respect to the various differential expression tools. But as some DE tools use slightly different column naming conventions, care should be taken to assure the correct column names are used for each DE tool.

Author(s)

Bob Morrison


robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.