ImmunePathwayLists: Immune Pathways with Corresponding Gene Markers

Description Usage Format Source Examples

Description

This matrix gives a predefined set of marker genes for many immune response pathways, as assembled by Brian Modena (a member of Daniel R Salomon's lab at Scripps Research Institute), and colleagues. It is used with userListEnrichment to search user-defined gene lists for enrichment.

Usage

1

Format

A 3597 x 2 matrix of characters containing Gene / Category pairs. The first column (Gene) lists genes corresponding to a given category (second column). Each Category entry is of the form <Immune Pathway>__ImmunePathway. Note that the matrix is sorted first by Category and then by Gene, such that all genes related to the same category are listed sequentially.

Source

For more information about this list, please see userListEnrichment

Examples

1
2

Example output

Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust


==========================================================================
*
*  Package WGCNA 1.61 loaded.
*
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=2
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=2
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

     Gene     Category              
[1,] "ATF2"   "4-1BB__ImmunePathway"
[2,] "CHUK"   "4-1BB__ImmunePathway"
[3,] "IFNG"   "4-1BB__ImmunePathway"
[4,] "IKBKAP" "4-1BB__ImmunePathway"
[5,] "IKBKB"  "4-1BB__ImmunePathway"
[6,] "IKBKE"  "4-1BB__ImmunePathway"

WGCNA documentation built on March 1, 2021, 1:05 a.m.