read_bam_to_countmatrix: read_bam_to_countmatrix
In ShirinG/exprAnalysis: A package for analysing RNA-seq and expression array data

Description Usage Arguments Details Value

Reads in bam files and creates a count matrix based on a gtf file.

1 2	read_bam_to_countmatrix(sampleTable, gtffile, projectfolder = getwd(), outPrefix, singleEnd = FALSE, ignore.strand = TRUE, fragments = TRUE)

`sampleTable`	Sample Table. See Vignette for instructions on how to build this data frame.
`gtffile`	GTF file.
`projectfolder`	File path where to save the output to. Defaults to working directory. Here, it saves the output to a subfolder called "Networks".
`outPrefix`	Prefix added to output name.
`singleEnd`	A logical indicating if reads are single or paired-end. In Bioconductor > 2.12 it is not necessary to sort paired-end BAM files by qname. When counting with summarizeOverlaps, setting singleEnd=FALSE will trigger paired-end reading and counting. It is fine to also set asMates=TRUE in the BamFile but is not necessary when singleEnd=FALSE.
`ignore.strand`	A logical indicating if strand should be considered when matching.
`fragments`	A logical; applied to paired-end data only. fragments controls which function is used to read the data which subsequently affects which records are included in counting. When fragments=FALSE, data are read with readGAlignmentPairs and returned in a GAlignmentPairs class. This class only holds 'mated pairs' from opposite strands; same-strand pairs singletons, reads with unmapped pairs and other fragments are dropped. When fragments=TRUE, data are read with readGAlignmentsList and returned in a GAlignmentsList class. This class holds 'mated pairs' as well as same-strand pairs, singletons, reads with unmapped pairs and other fragments. Because more records are kept, generally counts will be higher when fragments=TRUE. The term 'mated pairs' refers to records paired with the algorithm described on the ?readGAlignmentsList man page.