qtl2ggplot (version 1.2.6)

summary_scan1: 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 scan1
summary(object, ...)

Value

tbl summary

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

Author

Brian S Yandell,

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)