find_depleted_features: CircRNA feature selection

In stiv1n/CYCLeR: CircRNA transcriptome assembly tool

CircRNA feature selection

Description

CircRNA feature selection

Usage

find_depleted_features(circ_fc_adj, sample_table, circ_sg, test = "DEX")

Arguments

circ_fc_adj	count matrix corresponding to the circRNA features
sample_table	sample table formatted according to the manual, Must contain “sample_name” “treatment” “file_bam” “lib_size” “read_len”; NB the values in column “treatment” can only be “control” and “enriched”
circ_sg	SGSeq object supplying feature info
test	either “DEX” for DEXSeq based feature selection or “comparison” simple average comaparison

Details

This function works in 2 ways: direct comparison of average quantities or as a wrapper of DEXSeq. In case of dataset with replicates, the suggested approach is the use of DEXSeq statistical test.

Value

vector of featureID

Author(s)

Stefan Stefanov

stiv1n/CYCLeR documentation built on Sept. 15, 2022, 4:39 p.m.