clinicalEnrichment {maftools} | R Documentation |
Performs paiwise and groupwise fisher exact tests to find differentially enriched genes for every factor within a clinical feature.
clinicalEnrichment(maf, clinicalFeature = NULL, annotationDat = NULL, minMut = 5, useCNV = TRUE)
maf |
|
clinicalFeature |
columns names from 'clinical.data' slot of |
annotationDat |
If MAF file was read without clinical data, provide a custom |
minMut |
Consider only genes with minimum this number of samples mutated. Default 5. |
useCNV |
whether to include copy number events. Only applicable when MAF is read along with copy number data. Default TRUE if available. |
result list containing p-values
## Not run: laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools') laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') laml = read.maf(maf = laml.maf, clinicalData = laml.clin) clinicalEnrichment(laml, 'FAB_classification') ## End(Not run)