README.md

In stephenturner/msigdf: MSigDB in a data frame

MSigDF

The Molecular Signatures Database (MSigDB) in a data frame.

Current version: v5.2 (October 2016). For a more up-to-date version, see ToledoEM's fork at ToledoEM/msigdf.

Installation

# Install devtools if you don't already have it
install.packages("devtools")

# Just get the data
devtools::install_github("stephenturner/msigdf")

# Get the data and build the vignette (requires tidyverse, knitr, rmarkdown)
devtools::install_github("stephenturner/msigdf", build_vignettes = TRUE)

Example usage

See the package vignette for more.

library(dplyr)
library(msigdf)
vignette("msigdf")

msigdf.human %>% 
  filter(collection=="hallmark") %>% 
  head

  collection                          geneset entrez
1   hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB   3726
2   hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB   2920
3   hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB    467
4   hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB   4792
5   hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB   7128
6   hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB   5743

msigdf.human %>% filter(geneset=="KEGG_NON_HOMOLOGOUS_END_JOINING")

   collection                         geneset entrez
1          c2 KEGG_NON_HOMOLOGOUS_END_JOINING   7518
2          c2 KEGG_NON_HOMOLOGOUS_END_JOINING   4361
3          c2 KEGG_NON_HOMOLOGOUS_END_JOINING  27343
4          c2 KEGG_NON_HOMOLOGOUS_END_JOINING  27434
5          c2 KEGG_NON_HOMOLOGOUS_END_JOINING 731751
6          c2 KEGG_NON_HOMOLOGOUS_END_JOINING  79840
7          c2 KEGG_NON_HOMOLOGOUS_END_JOINING   3981
8          c2 KEGG_NON_HOMOLOGOUS_END_JOINING   2237
9          c2 KEGG_NON_HOMOLOGOUS_END_JOINING   1791
10         c2 KEGG_NON_HOMOLOGOUS_END_JOINING   7520
11         c2 KEGG_NON_HOMOLOGOUS_END_JOINING  10111
12         c2 KEGG_NON_HOMOLOGOUS_END_JOINING   2547
13         c2 KEGG_NON_HOMOLOGOUS_END_JOINING   5591
14         c2 KEGG_NON_HOMOLOGOUS_END_JOINING  64421

See the package vignette for more.

stephenturner/msigdf documentation built on May 30, 2019, 3:35 p.m.