get_targets: Get microRNA targets

In MahShaaban/sqlome: Build SQLite tables of microRNAs and Transcription Factors-gene Correlations

Description

This function uses the targetscan database annotations to get the microRNA gene and protien tragets. For microRNA-gene targets it is a straight forward subsetting the database and converting to ta tidy data.frame with the appropriate IDs. For microRNA-protein targets, it first obtain the gene targets as explained and then change transform the IDs to the corresponding protein/antibody IDs provided by the manufacturers of the used assays.

Usage

get_targets(mirna, feature_type = "gene")

Arguments

mirna	A charachter vector of the names of microRNAs of interes
feature_type	A character string to choose the desired type of annotations. Takes one of 'gene' or 'protein'.

Value

A tidy data.frame of microRNA in one column 'mirna_base' and targets column 'feature'. When used with the 'protein' another column is added to distinguish the feature_types genes or proteins.

Examples

mirna_base <- c("hsa-let-7a", "hsa-let-7b", "hsa-let-7c")
gene <- get_targets(mirna_base, 'gene')
ptn <- get_targets(mirna_base, 'protein')

MahShaaban/sqlome documentation built on May 28, 2019, 1:46 p.m.