get_gene_expression: This function get gene expression data of specific tissues...

In mqzhanglab/wHC: Goodness of fit Statistics Calculation based on weighted p-values

This function get gene expression data of specific tissues from GTEx

Description

The data resources comes from tpm of genes counts of RNAseq data of GTEx (gtexportal.org/home/datasets). It based on GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_tpm.gct.gz (Retrive Nov (2013))

Usage

get_gene_expression(
  gene_label = "ensembl_gene_id",
  tissue = support_gtex_tissue(),
  comb = "none"
)

Arguments

gene_label	is the gene names of the returning vector or matrix.It can be "ensembl_gene_id" or "symbols"
tissue	a vector of filters the expression level of specific tissues. Use support_gtex_tissue() to see supported tissues.
comb	is the operation on combining selected categories of tissues. It can be "median","mean","max","min",and "none", which calculate the median, mean of genes or do nothing on them.

Value

the numeric vector or matrix(@param mode is "none") representing prior information for each single gene

References

Lonsdale, John, et al. "The genotype-tissue expression (GTEx) project." Nature genetics 45.6 (2013): 580.

Examples

prior_expression=get_gene_expression(gene_label="symbols",tissue=c("Liver","Lung"),comb="mean")
prior_expression=get_gene_expression()

mqzhanglab/wHC documentation built on April 1, 2022, 6:28 p.m.