data.validate.genes: data.validate.genes

In cvraut/iBAGpkg: integrative Bayesian Analysis of the Genome

data.validate.genes

Description

Validates mrna and upstream data to ensure genes match.

Usage

data.validate.genes(mrna,data)

For each dataset the patient vector is assumed to be the rownames.

Arguments

mrna	:mrna data (follow convention of demo_mrna)
data	:list of other dataframes (follow demo conventions)
sep	("_"): the character seperator to use to differentiate mutliple columns of data per gene
DEBUG	FALSE: flag to print debug statements

Details

This function checks:

• all genes are unique in mrna

• all columns are unique across all datasets

• given an upstream data platform:

  • for each gene in mrna there is at least 1 gene present

  • upstream platforms do not contain genes which are not present in mrna

A match across gene makes use of the sep argument. First a regex is constructed from the mrna such as r"GENE(SEP.+)?" then all gene data is found by matching this pattern.

Note: gene names are automatically converted to strings

Note: SEP should not be able to be found in any of the genes from mrna (auto-fail if sep="")

Note: if SEP == NULL then this method will perform perfect matches similar to data.validate.patient

Note: the order of the genes don't have to match, but it is important that the contents do.

Value

boolean: whether this set of iBAG data is valid for the genes only

cvraut/iBAGpkg documentation built on July 26, 2022, 9:55 p.m.