remove_noise_from_bams: Function to remove the noisy reads from the BAM files

In noisyr: Noise Quantification in High Throughput Sequencing Output

Description

This function is used to remove the noisy reads from the BAM files. It uses as input the BAM file names, a gene table (usually containing individual exons, made using cast_gtf_to_genes), an expression matrix for each of these genes and a vector of abundance thresholds.

Usage

remove_noise_from_bams(
  bams,
  genes,
  expression,
  noise.thresholds,
  destination.files = base::paste0(base::basename(bams), ".noisefiltered.bam"),
  filter.by = c("gene", "exon"),
  make.index = FALSE,
  unique.only = TRUE,
  mapq.unique = 255,
  ...
)

Arguments

bams	a character vector of the BAM file names
genes	a tibble of the exons extracted from the gtf file; (usually the the output of cast_gtf_to_genes)
expression	the expression matrix or expression summary list, as calculated by calculate_expression_similarity_transcript
noise.thresholds	a vector of expression thresholds by sample; must be the same length as the number of BAM files, or a singular value to be used as a fixed noise threshold
destination.files	names for the output denoised BAM files; by default the same as the original files, appended with ".noisefiltered.bam", but created in the working directory
filter.by	Either "gene" (default) or "exon"; if filter.by="gene", a gene is removed from all BAM files if and only if all of its exons are below the corresponding noise thresholds; if filter.by="exon", then each exon is individually removed (from all samples) if it is below the corresponding noise thresholds.
make.index	whether a BAM index should be generated; if this is FALSE (the default) and no index exists, the function will exit with an error; the index needs to have the same name as each BAM file, but ending with .bam.bai
unique.only	whether only uniquely mapped reads should contribute to the expression of a gene/exon; default is TRUE
mapq.unique	The values of the mapping quality field in the BAM file that corresponds to uniquely mapped reads; by default, values of 255 are used as these correspond to the most popular aligners, but an adjustment might be needed; the mapq scores should be as follows: 255 for STAR, 60 for hisat2, 255 for bowtie in -k mode, 40 for bowtie2 default, 50 for tophat
...	arguments passed on to other methods

Value

Returns a matrix of the same dims as the expression matrix, with the noise removed. This matrix has no entries remaining below the noise threshold.

See Also

remove_noise_from_matrix

Examples

bams <- rep(system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE), 2)
genes <- data.frame("id" = 1:2,
                    "gene_id" = c("gene1", "gene2"),
                    "seqid" = c("seq1", "seq2"),
                    "start" = 1,
                    "end" = 1600)
noise.thresholds <- c(0, 1)
expression.summary = calculate_expression_similarity_transcript(
  bams = bams,
  genes = genes,
  mapq.unique = 99
)
remove_noise_from_bams(
    bams = bams,
    genes = genes,
    expression = expression.summary,
    noise.thresholds = noise.thresholds,
    destination.files = paste0(tempdir(), "/", basename(bams), ".noisefiltered.bam"),
    mapq.unique = 99
)

noisyr documentation built on April 16, 2021, 5:07 p.m.