get_tissuegenes: Obtain a tissue-specific list of genes for a pathway

In Sabor117/PathWAS: Creates predictive models of biological pathway functionality

Obtain a tissue-specific list of genes for a pathway

Description

Returns a series of gene lists for either all tissues in the GTEx transcriptomics dataset or for a specific tissue.

Usage

get_tissuegenes(
  exprn_data,
  in_genelist,
  all_simple_paths,
  in_tissue = NULL,
  tpm_threshold = 1
)

Arguments

exprn_data	data frame. The GTEx TPM file having been read in as a data frame.
in_genelist	data frame. A table of all genes in the pathway including a column with kegg_id (hsa:<ENTREZ>) and external_gene_name (gene name) as defined by BioMart
all_simple_paths	list. The list of all "simple" linear paths through a pathway to a chosen end-point.
in_tissue	character. Either NULL (and output a gene list for all tissues in GTEx) or a single specific tissue (the name must match the file names for the tissue in GTEx).
tpm_threshold	numeric. Threshold defining whether a gene is expressed or not. Default = 1

Details

This is a higher level function for creating one or multiple gene-lists for tissue-specific expression of genes. This is based on the GTEx Transcripts Per Million data (which can be found here: https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz). From this data we define a threshold (default = 1) constituting "above basal expression" of the gene. Any gene above this threshold is considered to be "expressed" in the defined tissue. The function then uses the linear paths provided from the smple_paths function and excludes any simple path which has at one or more genes with an expression level below the defined threshold (under the assumption that with one of the links in the chain missing, this is no longer a viable route for pathway functionality). Thus the output from this is not just only the genes which are expressed in a specific tissue, but also theoretically will exclude those genes which can only influence the desired end-point through genes which are defined as not being expressed within that tissue.

This function requires several inputs. It requires the GTEx TPM files, the input gene-list must come in the format of a column with kegg_id (this can be updated to be ENTREZ IDs) and external_gene_name (from BioMart). It also requires the output from smple_paths() under the assumption of having kept the connections between each gene and not just the names of the genes.

There default running option for this function provides the gene list for all tissues in the GTEx TPM files, however individual tissues can be selected. There is currently no option for selecting multiple or a list of tissues (this may be updated down the line).

Sabor117/PathWAS documentation built on Nov. 29, 2024, 7:44 a.m.