run_annoqtl: Annotate QTL intervals.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

QTL intervals in a HDF5 scan file are annotated with features from the GFF annotation file, and a copy of the HDF5 scan file is output, in which QTL feature annotation has been added. The GFF annotation file must relate to the same reference genome as was used in QTL analysis. In addition, physical positions of QTL intervals must be present, either directly in the QTL intervals themselves, or indirectly by pairing coordinates in the cross genetic map to a corresponding physical map. QTL intervals can be annotated for specific phenotypes and analyses with the pheno and scans parameters, respectively.

Usage

run_annoqtl(infile = NA_character_, annofile = NA_character_,
  outfile = NA_character_, pheno = character(), scans = character())

Arguments

infile	input HDF5 scan file [required]
annofile	GFF annotation file [required]
outfile	annotated HDF5 scan file [required]
pheno	phenotypes [default: all]
scans	analyses [default: all]

See Also

Other pipeline functions: run_digest, run_estimap, run_interptimes, run_makecross, run_makegeno, run_prep, run_pullmap, run_pushmap, run_recode, run_report, run_scanone, run_scantwo

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.