R: Create a gene table from a sleuth object

sleuth_gene_table

R Documentation

Create a gene table from a sleuth object

Description

Take in a sleuth object with added genes, and return a data table in which genes list the most significant transcript mapping to themselves

Usage

sleuth_gene_table(obj, test, test_type = "lrt", which_model = "full",
  which_group = "ens_gene")

Arguments

`obj`	a `sleuth` object
`test`	a character string denoting which beta to use
`test_type`	either 'wt' for Wald test or 'lrt' for likelihood ratio test
`which_model`	a character string denoting which model to use
`which_group`	a character string denoting which gene group to use

Value

a data.frame with the following columns

gene name; if ext_gene name specified, it will be legible gene name. If ens_gene name, it will be an Ensemble gene (assuming user followed the vignette)

most_sig_trancript: Most significant transcript for the given gene

pval: p-value for the test chosen

qval: False discovery rate normalized p-value (Benjamini-Hochberg, see: p.adjust)

num_transcripts: Total number of transcripts for the given gene

list_of_transcripts: All transcripts associated with this gene

Examples

sleuth_genes <- sleuth_gene_table(so, 'conditionIP', test_type ='wt',
                                  which_group = 'ext_gene')
head(sleuth_genes) # show info for first 5 genes
sleuth_genes[1:5, 6] # show transcripts for first 5 genes