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

In stemangiola/tidyBulk: Brings transcriptomics to the tidyverse

Creates a 'tt' object from a list of file names of BAM/SAM

Description

tidybulk_SAM_BAM() creates a 'tt' object from A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))

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 specifying an in-built annotation used for read summarization. It has four possible values including "mm10", "mm9", "hg38" and "hg19"
...	Further parameters passed to the function Rsubread::featureCounts

Details

'r lifecycle::badge("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

stemangiola/tidyBulk documentation built on Nov. 21, 2024, 8:14 a.m.