| summary.scanone {qtl} | R Documentation |
Print the rows of the output from scanone that
correspond to the maximum LOD for each chromosome, provided that they
exceed some specified thresholds.
## S3 method for class 'scanone':
summary(object, threshold,
format=c("onepheno", "allpheno", "allpeaks"),
perms, alpha, lodcolumn=1, pvalues=FALSE, df=FALSE, ...)
object |
An object output by the function
scanone. |
threshold |
LOD score thresholds. Only peaks with LOD score above
this value will be returned. This could be a single number or (for
formats other than "onepheno") a threshold for each LOD score
column. If alpha is specified, threshold should not be. |
format |
Format for the output; used only if there is more than one LOD score column in the input. See Details, below. |
perms |
Optional permutation results used to derive thresholds or
to calculate genome-scan-adjusted p-values. This must be consistent
with the object input, in that it must have the same number of
LOD score columns. |
alpha |
If perms are included, this is the significance level used
to calculate thresholds for determining which peaks to pull out.
If threshold is specified, alpha should not be. |
lodcolumn |
If format="onepheno", this indicates the LOD
score column to focus on. This should be a single number between 1
and the number of LOD columns in the object input. |
pvalues |
If TRUE, include columns with genome-scan-adjusted
p-values in the results. This requires that perms be
provided. |
df |
If TRUE, the degrees of freedom associated with the LOD scores are shown. |
... |
Ignored at this point. |
This function is used to report loci deemed interesting from a one-QTL
genome scan (by scanone).
For format="onepheno", we focus on a single LOD score column,
indicated by lodcolumn. The single largest LOD score peak on
each chromosome is extracted. If threshold is specified, only
those peaks with LOD meeting the threshold will be
returned. If perms and alpha are specified, a threshold
is calculated based on the permutation results in perms for the
significance level alpha. If neither threshold nor
alpha are specified, the peak on each chromosome is returned.
Again note that with this format, only the LOD score column indicated
by lodcolumn is considered in deciding which chromosomes to
return, but the LOD scores from other columns, at the position with
maximum LOD score in the lodcolumn column, are also returned.
For format="allpheno", we consider all LOD score columns, and
pull out the position, on each chromosome, showing the largest LOD
score. The output thus may contain multiple rows for a chromosome.
Here threshold may be a vector of LOD score thresholds, one for
each LOD score column, in which case only those positions for which a
LOD score column exceeded its threshold are given. If
threshold is a single number, it is applied to all of the LOD
score columns. If alpha is specified, it must be a single
significance level, applied for all LOD score columns, and again
perms must be specified, and these are used to calculate the
LOD score threshold for the significance level alpha.
For format="allpeaks", the output will contain, for each
chromosome, the maximum LOD score for each LOD score column, at the
position at which it achieved its maximum. Thus, the output will
contain no more than one row per chromosome, but will contain the
position and maximum LOD score for each of the LOD score columns.
The arguments threshold and alpha may be specified as
for the "allpheno" format. The results for a chromosome are
returned if at least one of the LOD score columns exceeded its
threshold.
If pvalues=TRUE, and perms is specified,
genome-scan-adjusted p-values are calculated for each LOD score
column, and there are additional columns in the output containing
these p-values.
In the case that X-chromosome specific permutations were performed
(with perm.Xsp=TRUE in scanone), autosome-
and X-chromosome specific thresholds and p-values are calculated by
the method in Broman et al. (in press).
An object of class summary.scanone, to be printed by
print.summary.scanone.
Karl W Broman, kbroman@biostat.wisc.edu
Broman, K. W., Sen, 'S, Owens, S. E., Manichaikul, A., Southard-Smith, E. M. and Churchill G. A. The X chromosome in quantitative trait locus mapping. Genetics, to appear.
scanone, plot.scanone,
max.scanone, subset.scanone,
c.scanone, summary.scanoneperm
c.scanoneperm
data(fake.bc) fake.bc <- calc.genoprob(fake.bc, step=5) # genome scan by Haley-Knott regression out <- scanone(fake.bc, method="hk") # permutation tests ## Not run: operm <- scanone(fake.bc, method="hk", n.perm=1000) ## End(Not run) # peaks for all chromosomes summary(out) # results with LOD >= 3 summary(out, threshold=3) # the same, but also showing the p-values summary(out, threshold=3, perms=operm, pvalues=TRUE) # results with LOD meeting the 0.05 threshold from the permutation results summary(out, perms=operm, alpha=0.05) # the same, also showing the p-values summary(out, perms=operm, alpha=0.05, pvalues=TRUE) ##### summary with multiple phenotype results out2 <- scanone(fake.bc, pheno.col=1:2, method="hk") # permutations ## Not run: operm2 <- scanone(fake.bc, pheno.col=1:2, method="hk", n.perm=1000) ## End(Not run) # results with LOD >= 2 for the 1st phenotype and >= 1 for the 2nd phenotype # using format="allpheno" summary(out2, thr=c(2, 1), format="allpheno") # The same with format="allpeaks" summary(out2, thr=c(2, 1), format="allpeaks") # The same with p-values summary(out2, thr=c(2, 1), format="allpeaks", perms=operm2, pvalues=TRUE) # results with LOD meeting the 0.05 significance level by the permutations # using format="allpheno" summary(out2, format="allpheno", perms=operm2, alpha=0.05) # The same with p-values summary(out2, format="allpheno", perms=operm2, alpha=0.05, pvalues=TRUE) # The same with format="allpeaks" summary(out2, format="allpeaks", perms=operm2, alpha=0.05, pvalues=TRUE)