read_rm: Read RepeakMasker output

In dwinter/repeatR: Parse and analyse RepeatMasker output

Description

Read RepeakMasker output

Usage

read_rm(file, tibble = FALSE, keep_order = TRUE, include_secondary = FALSE)

Value

A data.frame in which each row represents a (portion of) and alignment between a query sequence (usually a genome) and a reference repeat. Columns are

• score score The Smith-Waterman score for this alignment-section

• p_sub proportion of mismatches (substitutions)

• p_del propotion of deletions relative to target

• p_ins proportions of insertins relative to target

• qname query (usually chromosome or scaffold) name

• qstart start position in query sequence

• qend end position in query sequence

• qextend query sequence remaining after alignment

• complement is the alignment reverse and complement ("C") or same strnd ("+")

• tname target (repeat) name

• tclass target (repeat) class

• tstart start position in target sequence

• tend end position in target sequence

• textend target sequence remaining after alignment

• ID alignment ID (can be shared by multiple rows if targets interrupt each other)

• ali_type alignment type (primary for best alignment for this query region, secondary for others)

dwinter/repeatR documentation built on April 2, 2021, 7:31 p.m.