SLAPE.readDataset: Reading genomic evant dataset

In saezlab/SLAPenrich: Sample-population Level Analysis of Pathway enrichments

Description

This function reads a genomic dataset from a csv file and it stores it into an integer matrix. Row names of this matrix are official gene symbols and column names are sample identifiers. A non-zero entry in the i,j position indicates the presence of somatic mutation hosted by the i-th gene in the j-th sample (if the matrix is binary) or the number of point mutations hosted by the i-th gene in the j-th sample (if the matrix contains integers).

Usage

SLAPE.readDataset(filename)

Arguments

filename

The path of the csv file to be read and stored in the genomic event matrix.

Value

An integer matrix modeling a genomic event dataset. Row names of this matrix are official gene symbols and column names are sample identifiers. A non-zero entry in the i,j position indicates the presence of a somatic mutation hosted by the i-th gene in the j-th sample (if the matrix is binary) or the number of point mutations hosted by the i-th gene in the j-th sample (if the matrix contains integers).

Author(s)

Francesco Iorio - [e-mail]

saezlab/SLAPenrich documentation built on May 29, 2019, 12:57 p.m.