Preform Gene Set Enrichment Analysis using marker genes
doFeatureSetEnrichment(
dryrun = TRUE,
path_to_GSEA = NULL,
GSEA_dataset = NULL,
GSEA_ranked_file = NULL,
output_folder = NULL,
name_analysis_folder = "my_GSEA_analysis",
collapse = "false",
mode = c("Abs_max_of_probes", "Max_probe", "Median_of_probes", "Mean_of_probes",
"Sum_of_probes"),
norm = "meandiv",
nperm = 1000,
scoring_scheme = "weighted",
plot_top_x = 20,
set_max = 500,
set_min = 15
)do a dry run, default TRUE.
path to GSEA command line executable, e.g. gsea-XXX.jar. See details (1.) for more information.
path to a Human/Mouse collection from GSEA, e.g. Hallmarks C1. See details (2.) for more information.
path to .rnk file for GSEA. See details (3.) for more information
path to which the GSEA results will be saved. Default is current working directory.
default output subdirectory prefix to which results are saved. Will live within output_folder; equivalent of "Analysis Name" in GSEA Application.
only 'false' is supported. This will use your dataset as-is, in the original format.
option selected in Advanced Field "Collapsing Mode for Probe Sets => 1 gene"
normalization mode; only meandiv is supported.
number of permutations, default 1000
Default "weighted", equivalent of "enrichment statistic" in GSEA Application
Default 20, number of enrichment plots to produce.
default 500, equivalent to "max size; exclude larger sets" in Basic Fields in GSEA Application
default 15, equivalent to "min size; exclude smaller sets" in Basic Fields in GSEA Application
data.table
NECESSARY PREREQUISITES 1. download and install the COMMAND line (all platforms) gsea-XXX.jar https://www.gsea-msigdb.org/gsea/downloads.jsp 1.1. download zip file 1.2. unzip and move to known location (e.g. in path/to/your/applications/gsea/GSEA_4.3.2)
2. download the Human and Mouse collections https://www.gsea-msigdb.org/gsea/msigdb/index.jsp or zipped folder https://www.gsea-msigdb.org/gsea/downloads.jsp (all downloaded)
3. create ranked gene lists format: data.table or data.frame with 2 columns column 1 = gene symbols, column 2 = weight or rank metric for more details, see: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29
For more information on parameter conventions, please reference GSEA's documentation here: https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Syntax