STUDY_CANCER_GENES: Study k-mer composition of causal cancer genes from COSMIC...

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Study k-mer composition of causal cancer genes from COSMIC Cancer Gene Census (CGC) database.

Description

Detail of Cancer Gene Census can be accessed and read at https://cancer.sanger.ac.uk/census

Usage

STUDY_CANCER_GENES(
  cosmic.username,
  cosmic.password,
  tumour.type.regex = NULL,
  tumour.type.exact = NULL,
  cell.type = "somatic",
  genic.elements.counts.dt,
  output.dir = "study_cancer_genes/"
)

Arguments

cosmic.username	COSMIC username i.e. registered email.
cosmic.password	COSMIC password.
tumour.type.regex	Regular expression for "Tumour Types" column in Cancer Gene Census table. Default is NULL.
tumour.type.exact	Exact keywords for "Tumour Types" column in Cancer Gene Census table. Default is NULL.
cell.type	Type of cell: "somatic" or "germline". Default is "somatic".
genic.elements.counts.dt	Genic element count table generated from STUDY_GENIC_ELEMENTS.
output.dir	A directory for the outputs.

Value

An output directory containing plots.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.