test_gene_list_in_exposures {YAPSA} | R Documentation |
For all signatures found in a project, this function tests whether PIDs having mutations in a specified list of genes of interest have significantly higher exposures.
test_gene_list_in_exposures( in_gene_list, in_exposure_df, in_mut_table, in_gene.field = "GENE_short", in_p_cutoff = 0.05 )
in_gene_list |
List with genes of interest |
in_exposure_df |
Data frame with the signature exposures |
in_mut_table |
Data frame or table of mutations (derived from vcf-format) |
in_gene.field |
Name of the column in which the gene names are to be looked up |
in_p_cutoff |
Significance threshold |
A list with entries pvals
, exposure_df
,
number_of_mutated
,
pvals
: p-values of the
t-tests performed on mutated vs. unmutated PIDs
exposure_df
:
Transposed input exposures data frame with additional annotations for
mutation status
number_of_mutated
: Number of PIDs carrying a
mutation
NULL