stephenturner / msigdf

Molecular Signatures Database (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.

msigdf's Issues

html_document2 defunc

Hi when trying to install I am getting the following error:

* checking for file ‘/private/var/folders/sh/kwc66sqn4x36cjf9vncy99xm0000gp/T/Rtmpy2hUpm/devtools2a4d6079a2b6/stephenturner-msigdf-8330859/DESCRIPTION’ ... OK
* preparing ‘msigdf’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: processing vignette 'msigdf.Rmd' failed with diagnostics:
'html_document2' is defunct.
Use 'html_document' instead.
Execution halted

any ideas how to fix it?
How can I change it from html_document2 to html_document?

thanks

Get associated ID to (KEGG/GO/...)-term

Hi there,

I cannot open an issue at the updated repo from @ToledoEM. Hence I open it here.

Is it possible to retrieve next to the geneset term also the geneset ID?

E.g. For the term GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION the ID would be GO:0050434.

Thanks in advance,
Christian