run_scantwo: Do 2-QTL scan.
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Details Author(s) References See Also

Read cross data from the specified cross input file, run 2-dimensional QTL analysis using R/qtl scantwo (Broman et al. 2003), and write the results of that scan to the specified output file.

run_scantwo(infile = NA_character_, h5file = NA_character_,
  chr = character(), pheno = character(), model = c("normal", "binary"),
  method = c("em", "imp", "hk", "mr", "mr-imp", "mr-argmax"),
  n.perm = 1000L, n.cluster = 1L, alpha = NA_real_,
  thresholds = mapping(), step = 0, map.function = c("haldane", "kosambi",
  "c-f", "morgan"), error.prob = 1e-04, acovfile = NA_character_,
  icovfile = NA_character_)

`infile`	input cross file
`h5file`	scan result file
`chr`	sequences [default: all]
`pheno`	phenotypes [default: all]
`model`	phenotype model
`method`	method of QTL analysis
`n.perm`	number of permutations
`n.cluster`	number of threads
`alpha`	significance level for LOD thresholds
`thresholds`	fixed LOD thresholds
`step`	step size for genotype probabilities
`map.function`	genetic map function
`error.prob`	genotyping error rate
`acovfile`	additive covariates file
`icovfile`	interactive covariates file

If the input cross contains enumerated genotypes, marker regression is performed regardless of the value of the method parameter.

In typical usage, LOD threshold stringency can be set by the significance level (alpha), with a default value of 0.05. The significance level is used to estimate LOD thresholds from scantwo permutations.

This can be bypassed by setting six fixed LOD thresholds, along with a nominal significance level (alpha), in which case permutations are skipped and the fixed LOD thresholds are applied directly for assessing significance. When calling this function from the command line using Rscript, the thresholds parameter must be specified as a YAML string mapping scantwo LOD type names to threshold values (e.g. "full: 8, fv1: 7, int: 6, add: 5, av1: 4, one: 3"). When called from within the R environment, the thresholds parameter must be specified as a mapping object (e.g. mapping( c(full=8, fv1=7, int=6, add=5, av1=4, one=3) )).

Yue Hu

Thomas Walsh <tw164@protonmail.com>

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

R/qtl manual

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