read_BLAST_TCR_align_hits: Read the alignment output hit table .txt file from a TCR...

In mjdufort/TCRtools: Helper functions for analyzing TCR sequence data from single-cell RNA-seq

Description

Read in the alignment hit table file output by BLAST following a query of TCR sequences. This function reads and reformats the alignment results for downstream use. It expects the format output by the BLAST Download > Alignment > Hit Table(text).

Usage

read_BLAST_TCR_align_hits(
    filename, identity_threshold=100, length_threshold=100,
    query_seq_in_name=TRUE)

Arguments

filename	character string, the path and file name to read.
identity_threshold	numeric, the threshold for % identity match between the query and the subject sequences. Defaults to 100, can be reduced to allow less strict matching.
length_threshold	numeric, the threshold for % of the total length of the query sequence that must be found in the alignment. Defaults to 100, can be reduced to allow less strict matching. Setting to 0 or NULL results in no thresholding.
query_seq_in_name	logical, whether the alignment query sequence is included in the fasta query name. Alignment length thresholding requires the query sequence, which is assumed to be at the end of the query name.

Value

a data frame containing the alignment hits, optionally filtered by identity and length thresholds

mjdufort/TCRtools documentation built on Sept. 12, 2021, 7:11 p.m.