read.blast8: Read blast8 file(s) outputted by BLAT

In malnirav/hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

Given filename(s), the function reads the blast8 file format from BLAT as a data frame and performs basic score filtering if indicated. Any other file format will yield errors or erroneous results.

Usage

read.blast8(
  files = NULL,
  asGRanges = FALSE,
  removeFile = TRUE,
  parallel = FALSE
)

Arguments

files	blast8 filename, or vector of filenames, or a pattern of files to import.
asGRanges	return a GRanges object instead of a dataframe. Default is TRUE Saves memory!
removeFile	remove the blast8 file(s) after importing. Default is FALSE.
parallel	use parallel backend to perform calculation with BiocParallel. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using SerialParam.

Value

a dataframe or GRanges object reflecting blast8 file type.

Note

If parallel=TRUE, then be sure to have a parallel backend registered before running the function. One can use any of the following MulticoreParam SnowParam

See Also

pairwiseAlignSeqs, vpairwiseAlignSeqs, startgfServer, blatSeqs, read.psl

Examples

# this function works similar to read.psl #
#read.blast8(files="processed.*.blast8$")
#read.blast8(files=c("sample1hits.blast8","sample2hits.blast8"))

malnirav/hiReadsProcessor documentation built on July 29, 2021, 6:33 a.m.