validate.svc: Validate and reformat SV (structural variant) calls input

In gonzolgarcia/svpluscnv: Integrative analyses of CNV segmentation and SV variant calls

Description

This function validates and reformats SV (structural variant) calls input. It is used internally by 'svpluscnv' functions that require this type of data. A few formatting rules are enforced: 1) The input must obtain 8 columns in the following order(sample ID, chromosome of origin, strand of origin, position of origin,, chromosome of destination, strand of destination, position of destination, SV class) 2) SV classes accepted: DEL(deletion), DUP(duplication), INS(insertion), TRA(translocation), INV(inversion) and BND(break end) 3) Any variant in which chromosome of origin and destination differ are encoded as TRA (translocation) 4) pos1 < pos2 is enforced for all variants in which chromosome of origin and destination are the same 5) The class BND can be used to operate with complex events as long as both break ends are the same chromosome

Usage

validate.svc(sv.df)

Arguments

sv.df

(data.frame) structural variant table including the following fields: sample, chrom1, pos1, strand1, chrom2, pos2, strand2, svclass

Value

(data.frame) structural variant table with validated format for other svpluscnv operations; A unique id (uid) column is also added

Examples

validate.svc(sv.df)

gonzolgarcia/svpluscnv documentation built on March 4, 2020, 10:06 a.m.