genesFromTopTable: Extract a list (a character vector indeed) of genes from a...

In alexsanchezpla/geneLists: Extracts (sub)vectors or (sub)matrices from a limma "Top-table" applying user- defined filters

Description

Extract a list (a character vector indeed) of genes from a topTable outputted by the limma software

Usage

genesFromTopTable(aTopTable, filename = NULL, entrezOnly = TRUE,
  uniqueIds = TRUE, adjOrrawP = "adj", Pcutoff = 0.05, FCcutoff = 1,
  updown = "both", id2Select = "ENTREZ", cols2Select = 0)

Arguments

aTopTable	A top table file such as produced by the limma package or the UEB pipeline
filename	Name of the file that contains the topTable (to be used if the topTable is not in memory yet)
entrezOnly	To decide if only lines with a meaningful entrez symbol should be retained. Defaults to TRUE.
uniqueIds	To decide if duplicate identifiers should be removed after the selection defined by other parameters. Defaults to TRUE.
adjOrrawP	To decide if filtering is based on raw or adjusted p-values. Defaults to 'adj'.
Pcutoff	The filtering cutoff for p-values (if these are raw or adjusted is set by 'adjorRaw' parameter).
FCcutoff	The filtering cutoff for fold change.
updown	To decide which values to retain : up-regulated (FoldC >0 ), downregulated (FoldC < 0) or both. Defaults to 'both'.
id2Select	To decide which identifiers are to be selected. Defaults to 'ENTREZ'. Possible values are: ("ENTREZ","SYMBOL", NULL) but the alias ("Entrez", "EntrezsA", "Symbols", "SymbolsA") are accepted.
cols2Select	To decide which (and how many) columns are to be selected. Set 'cols2Select' to a (single or vector) value if no preferred identifier is known. It is used ony when 'id2select' is set to NULL. This parameter is dangerous because if more than 2 columns are selected the output is not a character vector and cannot be used as such.

See Also

limma

Examples

fileName<- system.file("extdata", "ExpressAndTop_AvsB.csv2", package = "geneLists")
AvsB <- read.table(fileName, header=TRUE, sep=";", dec=",", row.names=1)
entrezs_01_up  <- genesFromTopTable (AvsB, entrezOnly = TRUE, uniqueIds=TRUE, adjOrrawP = "adj", Pcutoff = 0.01, FCcutoff=1, updown="up", id2Select = "ENTREZ", cols2Select =0)
length(entrezs_01_up)
table_01_up  <- genesFromTopTable (AvsB, entrezOnly = TRUE, uniqueIds=TRUE, adjOrrawP = "adj", Pcutoff = 0.01, FCcutoff=1, updown="up", id2Select = NULL, cols2Select =1:3)
dim(table_01_up)

alexsanchezpla/geneLists documentation built on May 12, 2019, 7:41 a.m.