extraction_annotation_pos: This function generates two files as the final products....

In ginnyintifa/GPD:

Description

This function generates two files as the final products. First, mutations which result in protein-consequence with effect on proteins annotated; Second, mutations without protein-consequence.

Usage

extraction_annotation_pos(mutation_df, cancer_type, cancer_barcode,
  output_dir)

Arguments

mutation_df	Data frame of mc3 somatic mutations.
cancer_type	An identifier of cancer type, e.g. ACC,STAD,BRCA.
output_dir	The directory you would like to have your output files in.
cancer_barcod	A list of barcodes user wants to process, matching the last column of mutation file.

Examples

extraction_annotation_pos(mutation_df = sel_example_mutation,
                                 cancer_type = "example",
                                 cancer_barcode = sel_example_barcode,
                                 output_dir = "/Users/ginny/Google Drive/R_GPD/GPD_package_0401/example/")

ginnyintifa/GPD documentation built on Oct. 23, 2019, 1:52 a.m.