filter_host: Use Rsubread to align reads against one or more filter...

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

Use Rsubread to align reads against one or more filter libraries and subsequently remove mapped reads

Description

After aligning your sample to a target library with align_target(), use filter_host() to remove unwelcome host contamination using filter reference libraries. This function takes as input the name of the .bam file produced via align_target(), and produces a sorted .bam file with any reads that match the filter libraries removed. This resulting .bam file may be used upstream for further analysis. This function uses Rsubread. For the Rbowtie2 equivalent of this function, see filter_host_bowtie.

Usage

filter_host(
  reads_bam,
  lib_dir = NULL,
  libs,
  make_bam = FALSE,
  output = paste(tools::file_path_sans_ext(reads_bam), "filtered", sep = "."),
  subread_options = align_details,
  YS = 1e+05,
  threads = 1,
  quiet = TRUE
)

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().
lib_dir	Path to the directory that contains the filter Subread index files.
libs	The basename of the filter libraries (without index extension).
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.
output	The desired name of the output .bam or .csv.gz file. Extension is automatically defined by whether make_bam = TRUE. Default is the basename of unfiltered_bam + .filtered + extension.
subread_options	A named list specifying alignment parameters for the Rsubread::align() function, which is called inside align_target(). Elements should include type, nthreads, maxMismatches, nsubreads, phredOffset, unique, and nBestLocations. Descriptions of these parameters are available under ?Rsubread::align. Defaults to the global align_details object.
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 amount of threads available for the function. Default is 1 thread.
quiet	Turns off most messages. Default is TRUE.

Details

A compressed .csv can be created to produce a smaller output file that is created more efficiently and is still compatible with metascope_id().

Value

The name of a filtered, sorted .bam file written to the user's current working directory. Or, if make_bam = FALSE, a .csv.gz file containing a data frame of only requisite information to run metascope_id().

Examples

#### Filter reads from bam file that align to any of the filter libraries

## Assuming a bam file has been created previously with align_target()

## Create temporary directory
filter_ref_temp <- tempfile()
dir.create(filter_ref_temp)

## Download filter genome
all_species <- c("Staphylococcus aureus subsp. aureus str. Newman")
all_ref <- vapply(all_species, MetaScope::download_refseq,
                  reference = FALSE, representative = FALSE, compress = TRUE,
                  out_dir = filter_ref_temp, caching = FALSE,
                  FUN.VALUE = character(1))
ind_out <- vapply(all_ref, mk_subread_index, FUN.VALUE = character(1))

## Get path to example reads
readPath <- system.file("extdata", "subread_target.bam",
                        package = "MetaScope")

## Copy the example reads to the temp directory
refPath <- file.path(filter_ref_temp, "subread_target.bam")
file.copy(from = readPath, to = refPath)
utils::data("align_details")
align_details[["type"]] <- "rna"
align_details[["phredOffset"]] <- 10
# Just to get it to align - toy example!
align_details[["maxMismatches"]] <- 10

## Align and filter reads
filtered_map <- filter_host(
  refPath, lib_dir = filter_ref_temp,
  libs = stringr::str_replace_all(all_species, " ", "_"),
  threads = 1, subread_options = align_details)

## Remove temporary directory
unlink(filter_ref_temp, recursive = TRUE)

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