saveAldData: saveAldData: Save alignment depth plots for single genes
In rbamtools: Read and Write BAM (Binary Alignment) Files

Description Usage Arguments Author(s) See Also Examples

The function saveAldData reads alignment data for all genes in geneList sequentially from all Bam files listed in sampleBamFiles. The function cuts out intronic regions using the exonAlignDepth class and calculates a smoothed groupwise estimate using the exonLoessModel function. In a second region cutting step, remaining regions with low alignment depth are cut out using cutFlatAlignDepth. Finally, the function calculates group-wise ratios of alignment depth using the groupRatio function.

1	saveAldData(bs, gl, path, order=NULL, lim=1.1, startId=1, f=mean)

`bs`	sampleBamFiles. Contains BAM file names and group assignment.

`gl`	geneList. Contains a list of `geneModel` objects. Only gene-name, gene-id and global genetic region is used. Object construction can be abridged using `interior=FALSE`.

path

character. Base directory where output files are written to.

order

numeric. Defines order in which group-levels of sampleBamFiles object are used for groupRatio

lim

numeric. Limit used for groupRatio function. The percentage of genomic position where this limit is exceeded between all (ordered) group levels is given as gr (and cgr) value in aldrat table.

startId

numeric. Index used for first gene. Starting value for subsequent numbering of genes.

`f`	function. Function for calculation of group accumulates. Defaults to `mean`. Alternatively `median` may also be used.

Wolfgang Kaisers

bamReader

bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam, idx=TRUE)
# Extract data for HLHL17 gene:
seqid <- "chr1"
start <- 895967
end <- 901099
gene_name <- "HLHL17" # (optional)
ranges <- data.frame(seqid=seqid, start=start, end=end, gene_name=gene_name)
saveAldData(reader, ranges=ranges, filename="new_file.bam", f=mean)