sleuth_reliable_target_ids: List all the Sleuth object 'target_id's that have at least...

In nodrogluap/gumshoe: Supplemental Statistical Tests and Utilities for Kallisto/Sleuth RNASeq Analysis

List all the Sleuth object target_ids that have at least min_count_per_sample magnitude in the scaled est_count

Description

Can be used to provide a non-default target_ids paramater value in other methods of this package, effectively reducing the magnitude of multiple testing correction in statistical tests to restricting the reported tests to those transcripts with replicable expression levels (not potentially zero-inflated).

Usage

sleuth_reliable_target_ids(sleuth_obj, min_count_per_sample = 1)

Arguments

sleuth_obj	An existing Sleuth object as generated by sleuth_prep()
min_count_per_sample	threshold that all scaled est_counts for a transcript should have to be included im the results

Value

a list of target_ids meeting the given criterion

Examples

# Check the replicate dot plots for a factor combination (typically the control condition set, same number of columns as the dleuth object design_matrix, minus the intercept) 
replicate_dotplots(so,c(0,0))
# Note that many genes in the replicate samples have zero expression in one sample, but up to exp(4) in another. 
# Exclude these low-expressed genes from a U test to reduce pval inflation caused by multiple testing correction (qval/FDR)
sleuth_u(so, "age", 65, target_ids=sleuth_reliable_target_ids(so, exp(4)))

nodrogluap/gumshoe documentation built on Feb. 28, 2023, 6:15 p.m.