import.gs: Read in an AGS or FGS test file

In ashwini06/NEArender: Network Enrichment Analysis

Description

Imports a TAB-delimited AGS or FGS file. Checks the format of the given FGS file. Reads in unique gene/protein IDs from the given file tbl so that the created object can be directly submitted to nea.render and gsea.render. The function import.gs will be automatically called from nea.render if parameters AGS and/or FGS of the latter correspond to text files rather than lists.

Usage

import.gs(tbl, Lowercase = 1, col.gene = 2, col.set = 3, gs.type = "",
  header = FALSE)

Arguments

tbl	Input TAB-delimited FGS file.
Lowercase	render gene/protein IDs lower-case.
col.gene	Number of the column with gene/protein IDs in the input file.
col.set	Number of the column with set (sample, pathway etc.) IDs in the input file. Special options: col.set = 0: all gene/protein IDs in the file become members of a single FGS; col.set < 0 each single gene/protein IDs becomes a separate FGS (ID of which equals the gene/protein ID).
gs.type	GS type, 'a' produces AGS, 'f' produces FGS.
header	assign logical value (TRUE/FALSE) to consider the first line as header from the input file (default:FALSE).

Value

A list with entry names that correspond AGS/FGS IDs in the input file and gene/protein IDs as elements of each entry.

See Also

mutations2ags, samples2ags

Examples

data(can.sig.go)
fpath <- can.sig.go
fgs.list <- import.gs(fpath)
summary(fgs.list)

ashwini06/NEArender documentation built on May 17, 2019, 6:39 p.m.