read.blast8: Read blast8 file(s) outputted by BLAT
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description Usage Arguments Value Note See Also Examples

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.

1 2	read.blast8(files = NULL, asGRanges = FALSE, removeFile = TRUE, parallel = FALSE)

`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`.

a dataframe or GRanges object reflecting blast8 file type.

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

pairwiseAlignSeqs, vpairwiseAlignSeqs, startgfServer, blatSeqs, read.psl

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

hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.