readList: Read in gene set data as a named list

In gage: Generally Applicable Gene-set Enrichment for Pathway Analysis

Description

This function reads in gene set data in GMT (.gmt) format as a named list. GMT is defined originally by GSEA program. The code may be slightly revised for reading in gene set data in other tab-delimited formats too.

Usage

readList(file)

Arguments

file	character string, the full path name to the gene set data file in GMT format.

Value

A named list, each element is a character vector giving the gene IDs of a gene set.

Author(s)

Weijun Luo <[e-mail]>

References

Luo, W., Friedman, M., Shedden K., Hankenson, K. and Woolf, P GAGE: Generally Applicable Gene Set Enrichment for Pathways Analysis. BMC Bioinformatics 2009, 10:161

See Also

readExpData read in gene expression data

Examples

#an example GMT gene set data derived from MSigDB data
filename=system.file("extdata/c2.demo.gmt", package = "gage")
demo.gs=readList(filename)
demo.gs[1:3]
#to use these gene sets with gse16873, need to convert the gene symbols
#to Entrez IDs first
data(egSymb)
demo.gs.sym<-lapply(demo.gs, sym2eg)
demo.gs.sym[1:3]

Example output

$`3AB_GAMMA_DN`
 [1] "ANXA3"     "BNIP2"     "COLQ"      "CSAD"      "CSNK1A1"   "DDX3Y"    
 [7] "DPAGT1"    "FEN1"      "LOC653689" "MED31"     "NAT12"     "PTK9L"    
[13] "THOC4"    

$`4NQO_ESR_OLD_UNREG`
 [1] "EIF3S6IP" "FLOT1"    "GNPNAT1"  "HGF"      "LCK"      "NDRG1"   
 [7] "SLC18A2"  "SOX9"     "SYK"      "TAF1C"    "TP53I11" 

$`4NQO_ESR_WS_UNREG`
 [1] "ARPC1B"   "ATP5I"    "CEPT1"    "CNKSR1"   "COL17A1"  "CTCF"    
 [7] "CTGF"     "FLOT1"    "FUT4"     "GABBR1"   "GALNT2"   "GNPNAT1" 
[13] "HADH2"    "HGF"      "HLA-DQA1" "HNRPC"    "ITGB8"    "KIAA0146"
[19] "LCK"      "LRRFIP2"  "NDRG1"    "PDCD5"    "PRDX4"    "RHOB"    
[25] "SGCB"     "SGPL1"    "SOX7"     "SOX9"     "SYK"      "TAF1C"   
[31] "TP53I11"  "TTC19"    "TXNRD2"   "UGCG"     "USP1"     "ZNF507"  

$`3AB_GAMMA_DN`
 [1] "306"    "663"    "8292"   "51380"  "1452"   "8653"   "1798"   "2237"  
 [9] NA       "51003"  "122830" NA       "10189" 

$`4NQO_ESR_OLD_UNREG`
 [1] NA      "10211" "64841" "3082"  "3932"  "10397" "6571"  "6662"  "6850" 
[10] "9013"  "9537" 

$`4NQO_ESR_WS_UNREG`
 [1] "10095" "521"   "10390" "10256" "1308"  "10664" "1490"  "10211" "2526" 
[10] "2550"  "2590"  "64841" NA      "3082"  "3117"  NA      "3696"  "23514"
[19] "3932"  "9209"  "10397" "9141"  "10549" "388"   "6443"  "8879"  "83595"
[28] "6662"  "6850"  "9013"  "9537"  "54902" "10587" "7357"  "7398"  "22847"

gage documentation built on Dec. 13, 2020, 2:01 a.m.