tidybulk_SAM_BAM-methods: Creates a 'tt' object from a list of file names of BAM/SAM

In tidybulk: Brings transcriptomics to the tidyverse

Description

tidybulk_SAM_BAM() creates a 'tt' object from a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

Usage

tidybulk_SAM_BAM(file_names, genome = "hg38", ...)

## S4 method for signature 'character,character'
tidybulk_SAM_BAM(file_names, genome = "hg38", ...)

Arguments

file_names	A character vector
genome	A character string
...	Further parameters passed to the function Rsubread::featureCounts

Details

\lifecycle

maturing

This function is based on FeatureCounts package (DOI: 10.1093/bioinformatics/btt656). This function creates a tidybulk object and is useful if you want to avoid to specify .sample, .transcript and .abundance arguments all the times. The tidybulk object have an attribute called internals where these three arguments are stored as metadata. They can be extracted as attr(<object>, "internals").

Underlying core function Rsubread::featureCounts(annot.inbuilt = genome,nthreads = n_cores, ...)

Value

A 'tidybulk' object

A 'tidybulk' object

tidybulk documentation built on April 7, 2021, 6 p.m.