remove_matches | R Documentation |
Within 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.
remove_matches(reads_bam, read_names, output, YS, threads, aligner, make_bam)
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 |
read_names |
A |
output |
The name of the .bam or .rds 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 the creation of an intermediate fastq file. Default is 1000000. |
threads |
The number of threads to be used in filtering the bam file. |
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. An rds file will be created instead if |
This function is not intended for direct use.
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()
.
#readPath <- system.file("extdata", "subread_target.bam", # package = "MetaScope") ## Assume that the first 10 query names aligned to first filter library ## And another 10 aligned to second filter library # qnames <- Rsamtools::scanBam(readPath)[[1]]$qname # read_names <- list(qnames[1:10], qnames[30:40]) # out <- "subread_target.filtered.bam" # remove_matches_bam(readPath, read_names, out, YS = 1000, threads = 1, # aligner = "subread", make_bam = FALSE)
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