summary_scan1: Summary of scan1 object

In qtl2ggplot: Data Visualization for QTL Experiments

Summary of scan1 object

Description

Summary of scan1 object

Usage

summary_scan1(
  object,
  map,
  snpinfo = NULL,
  lodcolumn = seq_len(ncol(object)),
  chr = names(map),
  sum_type = c("common", "best"),
  drop = 1.5,
  show_all_snps = TRUE,
  ...
)

## S3 method for class 'scan1'
summary(object, ...)

Arguments

object	object from scan1
map	A list of vectors of marker positions, as produced by insert_pseudomarkers.
snpinfo	Data frame with SNP information with the following columns (the last three are generally derived from with index_snps): chr - Character string or factor with chromosome pos - Position (in same units as in the "map" attribute in genoprobs. sdp - Strain distribution pattern: an integer, between 1 and 2^n - 2 where n is the number of strains, whose binary encoding indicates the founder genotypes snp - Character string with SNP identifier (if missing, the rownames are used). index - Indices that indicate equivalent groups of SNPs. intervals - Indexes that indicate which marker intervals the SNPs reside. on_map - Indicate whether SNP coincides with a marker in the genoprobs
lodcolumn	one or more lod columns
chr	one or more chromosome IDs
sum_type	type of summary
drop	LOD drop from maximum
show_all_snps	show all SNPs if TRUE
...	other arguments not used

Value

tbl summary

Author(s)

Brian S Yandell, [e-mail]

Examples

# read data
iron <- qtl2::read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
# insert pseudomarkers into map
map <- qtl2::insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- qtl2::calc_genoprob(iron, map, error_prob=0.002)

# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- qtl2::get_x_covar(iron)

# perform genome scan
out <- qtl2::scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)

# summary
summary(out, map)

qtl2ggplot documentation built on March 31, 2023, 6:06 p.m.