tidybulk_SAM_BAM {tidybulk} | R Documentation

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

### 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

'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

[Package tidybulk version 1.4.0 Index]