find_peaks: Find peaks in a set of LOD curves

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Find peaks in a set of LOD curves

Description

Find peaks in a set of LOD curves (output from scan1()

Usage

find_peaks(
  scan1_output,
  map,
  threshold = 3,
  peakdrop = Inf,
  drop = NULL,
  prob = NULL,
  thresholdX = NULL,
  peakdropX = NULL,
  dropX = NULL,
  probX = NULL,
  expand2markers = TRUE,
  sort_by = c("column", "pos", "lod"),
  cores = 1
)

Arguments

scan1_output	An object of class "scan1" as returned by scan1().
map	A list of vectors of marker positions, as produced by insert_pseudomarkers(). Can also be an indexed SNP info table, as from index_snps() or scan1snps().
threshold	Minimum LOD score for a peak (can be a vector with separate thresholds for each lod score column in scan1_output)
peakdrop	Amount that the LOD score must drop between peaks, if multiple peaks are to be defined on a chromosome. (Can be a vector with separate values for each lod score column in scan1_output.)
drop	If provided, LOD support intervals are included in the results, and this indicates the amount to drop in the support interval. (Can be a vector with separate values for each lod score column in scan1_output.) Must be \le peakdrop
prob	If provided, Bayes credible intervals are included in the results, and this indicates the nominal coverage. (Can be a vector with separate values for each lod score column in scan1_output.) Provide just one of drop and prob.
thresholdX	Separate threshold for the X chromosome; if unspecified, the same threshold is used for both autosomes and the X chromosome. (Like threshold, this can be a vector with separate thresholds for each lod score column.)
peakdropX	Like peakdrop, but for the X chromosome; if unspecified, the same value is used for both autosomes and the X chromosome. (Can be a vector with separate values for each lod score column in scan1_output.)
dropX	Amount to drop for LOD support intervals on the X chromosome. Ignored if drop is not provided. (Can be a vector with separate values for each lod score column in scan1_output.)
probX	Nominal coverage for Bayes intervals on the X chromosome. Ignored if prob is not provided. (Can be a vector with separate values for each lod score column in scan1_output.)
expand2markers	If TRUE (and if drop or prob is provided, so that QTL intervals are calculated), QTL intervals are expanded so that their endpoints are at genetic markers.
sort_by	Indicates whether to sort the rows by lod column, genomic position, or LOD score.
cores	Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().

Details

For each lod score column on each chromosome, we return a set of peaks defined as local maxima that exceed the specified threshold, with the requirement that the LOD score must have dropped by at least peakdrop below the lowest of any two adjacent peaks.

At a given peak, if there are ties, with multiple positions jointly achieving the maximum LOD score, we take the average of these positions as the location of the peak.

Value

A data frame with each row being a single peak on a single chromosome for a single LOD score column, and with columns

• lodindex - lod column index

• lodcolumn - lod column name

• chr - chromosome ID

• pos - peak position

• lod - lod score at peak

If drop or prob is provided, the results will include two additional columns: ci_lo and ci_hi, with the endpoints of the LOD support intervals or Bayes credible wintervals.

See Also

scan1(), lod_int(), bayes_int()

Examples

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))


# insert pseudomarkers into map
map <- insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- 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 <- get_x_covar(iron)

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

# find just the highest peak on each chromosome
find_peaks(out, map, threshold=3)

# possibly multiple peaks per chromosome
find_peaks(out, map, threshold=3, peakdrop=1)

# possibly multiple peaks, also getting 1-LOD support intervals
find_peaks(out, map, threshold=3, peakdrop=1, drop=1)

# possibly multiple peaks, also getting 90% Bayes intervals
find_peaks(out, map, threshold=3, peakdrop=1, prob=0.9)

qtl2 documentation built on May 29, 2024, 11:46 a.m.