remove_matches: Helper function to remove reads matched to filter libraries

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Helper function to remove reads matched to filter libraries

Description

Using the filter_host() function, we align our sequencing sample to all filter libraries of interest. The remove_matches() function allows for removal of any target reads that are also aligned to filter libraries.

Usage

remove_matches(
  reads_bam,
  read_names,
  output,
  YS,
  threads,
  aligner,
  make_bam,
  quiet
)

Arguments

reads_bam	The name of a merged, sorted .bam file that has previously been aligned to a reference library. Likely, the output from running an instance of align_target().
read_names	A list of target query names from reads_bam that have also aligned to a filter reference library. Each list element should be a vector of read names.
output	The name of the .bam or .csv.gz file that to which the filtered alignments will be written.
YS	yieldSize, an integer. The number of alignments to be read in from the bam file at once for chunked functions. Default is 100000.
threads	The number of threads to be used in filtering the bam file. Default is 1.
aligner	The aligner which was used to create the bam file.
make_bam	Logical, whether to also output a bam file with host reads filtered out. A .csv.gz file will be created instead if FALSE. Creating a bam file is costly on resources over creating a compressed csv file with only relevant information, so default is FALSE.
quiet	Turns off most messages. Default is TRUE.

Details

This function is not intended for direct use.

Value

Depending on input make_bam, either the name of a filtered, sorted .bam file written to the user's current working directory, or an RDS file containing a data frame of only requisite information to run metascope_id().

compbiomed/MetaScope documentation built on Nov. 5, 2024, 9:25 p.m.