identify_expressed_genes: Identify expressed genes. Identify expressed genes based on...

In ys-amms/bionexr: Integrative network-based analysis of cancer somatic mutation and expression data

Description

Identify expressed genes. Identify expressed genes based on user-provided expression data.

Usage

identify_expressed_genes(df_user_exp, rsem_thres = 1, frac_thres = 0.5)

Arguments

df_user_exp	A dataframe.
rsem_thres	Default value is 1.
frac_thres	Default value is 0.5.

Examples

## Not run: 
mut_data <- firehose_get("HNSC", "mutation", run_date = "2015_08_21", run_type = "stddata")
mut_data <- mut_data[[1]]
mut_sample_ids <- unique(mut_data[[7]])

exp_data <- firehose_get("HNSC", "expression", run_date = "2015_08_21", run_type = "stddata")
exp_data <- exp_data[[1]]
exp_sample_ids <- colnames(exp_data)

common_case <- intersect(mut_sample_ids, exp_sample_ids)
exp_control <- grepl("-11$", exp_sample_ids)
hnsc_exp <- exp_data[, (exp_sample_ids %in% common_case) | exp_control]
expressed_genes <- identify_expressed_genes(hnsc_exp, rsem_thres = 1, frac_thres = 0.5)

## End(Not run)

ys-amms/bionexr documentation built on May 4, 2019, 5:33 p.m.