run_prep: Prepare data in 'R/qtl' CSV file.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

This script will take an R/qtl input data file, and prepare it for input to shmootl. Possible prep actions include resolving map sequence labels ('normseq'), estimating a new genetic map with the R/qtl function 'est.map' (Broman et al. 2003), jittering existing map positions with the R/qtl function 'jittermap' (Broman et al. 2003), and replacing empty cells with an explicit missing value symbol ('replace.missing').

If no prep actions are specified, map sequence labels are normalised; a genetic map is estimated if not found, otherwise the existing map is jittered; and empty cells are replaced with an explicit missing value. If one or more prep actions are specified, only the specified actions will be applied. It is the responsibility of the user to ensure that any changes are valid for a given input file.

Aside from prep actions, other options include 'require.mapunit', which indicates if the input file must contain explicit map units; and 'include.mapunit', which indicates if explicit map units should be included in the output file. Options 'error.prob' and 'map.function' are passed to the R/qtl function 'est.map', while option 'amount' is passed to the R/qtl 'jittermap' function.

Usage

run_prep(datafile = NA_character_, normseq = FALSE, estimap = FALSE,
  error.prob = 1e-04, map.function = c("haldane", "kosambi", "c-f",
  "morgan"), jittermap = FALSE, amount = 1e-06, replace.missing = FALSE,
  require.mapunit = FALSE, include.mapunit = TRUE)

Arguments

datafile	R/qtl CSV file [required]
normseq	normalise map sequence labels
estimap	estimate genetic map
error.prob	genotyping error rate
map.function	genetic map function
jittermap	jitter map positions
amount	jitter amount
replace.missing	make missing values explicit
require.mapunit	require map units in input
include.mapunit	include map units in output

References

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. (PubMed)

See Also

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

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