count_reads: Count reads in bam files using featureCounts
In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R

Description Usage Arguments Value Examples

Function to count reads mapping to a reference genome. Users can either supply their own reference or use the built-in one for hg19.

count_reads(featurecounts = "featureCounts", annotationFile = NULL,
  annotationFormat = "SAF", requireBothEndsMapped = TRUE,
  excludeChimeric = TRUE, pairedEnd = TRUE, pairInsertRange = NULL,
  countMultiMapping = FALSE, multiFeatureReads = FALSE, minQual = 0,
  stranded = 0, groupBy = NULL, featureType = NULL, threads = 1,
  ignoreDup = FALSE, outname = NULL, alignments = NULL)

`featurecounts`	Character string. Path to featureCounts
`annotationFile`	Character string. Path to annotation file. If NULL, the default hg19 genome is used.
`annotationFormat`	Specify the format of the annotation file. Acceptable formats include <e2><80><98>GTF<e2><80><99> and <e2><80><98>SAF<e2><80><99>. The in-built annotation is 'SAF'.
`requireBothEndsMapped`	Logical. If TRUE, only fragments that have both ends successfully aligned will be considered for summarization. This option should be used together with pairedEnd = TRUE.
`excludeChimeric`	Logical. If TRUE, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be counted. This option should be used together with pairedEnd = TRUE.
`pairedEnd`	Logical. If TRUE, fragments (or templates) will be counted instead of reads. This option is only applicable for paired-end reads.
`pairInsertRange`	Vector of two integers specifying the minimum and maximum fragment/template lengths. The default values are c(50, 600). Must be used together with pairedEnd = TRUE.
`countMultiMapping`	If TRUE, multi-mapping reads/fragments will be counted.
`multiFeatureReads`	Reads/fragments overlapping with more than one meta-feature/feature will be counted more than once. Note that when performing meta-feature level summarization, a read (or fragment) will still be counted once if it overlaps with multiple features within the same meta-feature (as long as it does not overlap with other metafeatures).
`minQual`	The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default.
`stranded`	Indicate if strand-specific read counting should be performed. Acceptable values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default. For paired-end reads, strand of the first read is taken as the strand of the whole fragment.
`groupBy`	Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes) when GTF annotation is provided. Default is 'gene id<e2><80><99>.
`featureType`	Specify the feature type. Only rows which have the matched feature type in the provided GTF annotation file will be included for read counting. Default is <e2><80><98>exon<e2><80><99>.
`threads`	Number of the threads. The value should be between 1 and 32. 1 by default.
`ignoreDup`	Logical. If TRUE, reads that were marked as duplicates will be ignored. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read.
`outname`	Character string. Name of the output file. The output file contains the number of reads assigned to each meta-feature or feature.
`alignments`	Character vector. Paths to BAM files.

Tab-delimited file containing the number of reads assigned to each meta-feature or feature and a matrix with the same.

## Not run: 
alignments <- list.files(path = "bam_files", pattern = "*.bam$")
threads <- parallel::detectCores() - 1
counts <- count_reads(featurecounts = "featureCounts", threads = threads,
                      alignments = alignments)

## End(Not run)