hiReadsProcessor (version 1.8.2)

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

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.

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"))