| Title: | Datasets for the R/qtl Book |
|---|---|
| Description: | Datasets for the book, A Guide to QTL Mapping with R/qtl. Broman and Sen (2009) <doi:10.1007/978-0-387-92125-9>. |
| Authors: | Karl W Broman [aut, cre]
|
| Maintainer: | Karl W Broman <[email protected]> |
| License: | GPL-3 |
| Version: | 0.18-10 |
| Built: | 2024-10-31 21:07:03 UTC |
| Source: | https://github.com/kbroman/qtlbook |
Anonymous data with a phenotype error and a pair of individuals with very similar phenotypes.
ch3ach3a
An object of class cross. See qtl::read.cross()
for details.
A backcross with 234 individuals, each with five phenotypes and typed at 166 markers.
Karl W Broman, [email protected]
Broman, K. W. and Sen, S. (2009) A Guide to QTL Mapping with R/qtl. Springer, New York.
data(ch3a) # phenotype problem pairs(ch3a$pheno) ch3a$pheno[ch3a$pheno[,4]==0,] # individual 159 # individuals with similar genotypes library(qtl) cg <- comparegeno(ch3a) hist(cg, breaks=200) max(cg[cg < 1]) which(cg == max(cg[cg < 1]), arr.ind=TRUE)data(ch3a) # phenotype problem pairs(ch3a$pheno) ch3a$pheno[ch3a$pheno[,4]==0,] # individual 159 # individuals with similar genotypes library(qtl) cg <- comparegeno(ch3a) hist(cg, breaks=200) max(cg[cg < 1]) which(cg == max(cg[cg < 1]), arr.ind=TRUE)
Anonymous data with markers showing severe segregation distortion.
ch3bch3b
An object of class cross. See qtl::read.cross()
for details.
An intercross with 144 individuals, each with one phenotype and typed at 145 markers.
Karl W Broman, [email protected]
Broman, K. W. and Sen, S. (2009) A Guide to QTL Mapping with R/qtl. Springer, New York.
data(ch3b) library(qtl) thetab <- geno.table(ch3b) plot(-log10(thetab[,ncol(thetab)]), ylab=expression(-log[10](P))) thetab[thetab[,ncol(thetab)] < 1e-6,]data(ch3b) library(qtl) thetab <- geno.table(ch3b) plot(-log10(thetab[,ncol(thetab)]), ylab=expression(-log[10](P))) thetab[thetab[,ncol(thetab)] < 1e-6,]
Anonymous data with markers out of place.
ch3cch3c
An object of class cross. See qtl::read.cross()
for details.
An intercross with 100 individuals, each with one real phenotype and typed at 108 markers.
Karl W Broman, [email protected]
Broman, K. W. and Sen, S. (2009) A Guide to QTL Mapping with R/qtl. Springer, New York.
data(ch3c) library(qtl) ch3c <- est.rf(ch3c) plotRF(ch3c, chr=c(1,7,12,13,15))data(ch3c) library(qtl) ch3c <- est.rf(ch3c) plotRF(ch3c, chr=c(1,7,12,13,15))
Data from a mouse intercross experiment on gut length, including both sexes.
All individuals carry the mutation.
gutlengthgutlength
An object of class cross. See qtl::read.cross()
for details.
A mouse intercross between C3HeBFeJ (C3) and C57BL/6J (B6), with one F1
parent carrying the mutation. There are 1068
mice from reciprocal intercrosses. Over 2000 mice were generated, but only
those individuals heterozygous at were genotyped
and included in the data set. is on chromosome 15, and so that
chromosome exhibits an unusual segregation pattern. Some mice received the
mutation from their mother and some from their father.
The primary phenotype here is gut length (in cm). The phenotype
cross indicates the cross used to generate an animal.
E. Michelle Southard-Smith, Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, [email protected]
Owens, S. E., Broman, K. W., Wiltshire, T., Elmore, J. B.,
Bradley, K. M., Smith, J. R. and Southard-Smith, E. M. (2005) Genome-wide
linkage identifies novel modifier loci of aganglionosis in the
model of Hirschsprung disease. Hum. Mol.
Genet. 14, 1549–1558.
Broman, K. W., Sen, \'S, Owens, S. E., Manichaikul, A., Southard-Smith, E. M. and Churchill G. A. (2006) The X chromosome in quantitative trait locus mapping. Genetics 174, 2151–2158.
iron, myocard, nf1,
ovar, trout
data(gutlength) library(qtl) plot(gutlength)data(gutlength) library(qtl) plot(gutlength)
Data from a mouse intercross experiment (using the C57BL/6J/Ola and SWR/Ola strains) on basal iron levels in the liver and spleen.
ironiron
An object of class cross. See qtl::read.cross()
for details.
An intercross with 284 individuals (including both sexes and both cross
directions), each with measures of iron (in ) in the
liver and spleen.
Andrew G. Smith, MRC Toxicology Unit, [email protected]
Grant, G. G., Robinson, S. W., Edwards, R. E., Clothier, B., Davies, R., Judah, D. J., Broman, K. W. and Smith, A. G. (2006) Multiple polymorphic loci determine basal hepatic and splenic iron status in mice. Hepatology 44, 174–185.
link{gutlength}, link{myocard}, link{nf1},
link{ovar}, link{trout}
data(iron) library(qtl) plot(iron)data(iron) library(qtl) plot(iron)
Data from a mouse intercross experiment on myocarditis.
myocardmyocard
An object of class cross. See qtl::read.cross()
for details.
An intercross between the H-2s congenic mice A.SW and B10.S, with 296 individuals (including both sexes). The mice were injected with purified murine cardiac myosin, and the area of infiltrated myocardium in heart sections was measured. The phenotype is the percent myocarditis.
Noel R. Rose, Department of Pathology, Johns Hopkins University, [email protected]
Guler, M. L, Ligons, D. L., Wang, Y., Bianco, M., Broman, K. W. and Rose, N. R. (2005) Two autoimmune diabetes loci influencing T cell apoptosis control susceptibility to experimental autoimmune myocarditis. J. Immunol. 174: 2167–2173.
link{gutlength}, link{iron}, link{nf1}
link{ovar}, link{trout}
data(myocard) library(qtl) plot(myocard)data(myocard) library(qtl) plot(myocard)
Data from a backcross experiment on neurofibromatosis type I. All individuals carry the NPcis mutation, received either from their mother or from their father.
nf1nf1
An object of class cross. See qtl::read.cross()
for details.
Backcrosses (C57BL/6J x A/J) x C57BL/6J and C57BL/6J x (A/J x C57BL/6J) with
a total of 254 individuals. Individuals received the NPcis mutation
from either their mother or their father (indicated by the phenotype
from.mom. The major phenotype, affected indicates whether the
mice were affected (1) or unaffected (0) with neurofibromatosis type 1.
Reilly, K. M., Broman, K. W., Bronson, R. T., Tsang, S., Loisel, D. A., Christy, E. S., Sun, Z., Diehl, J., Munroe, D. J. and Tuskan, R. G. (2006) An imprinted locus epistatically influences Nstr1 and Nstr2 to control resistance to nerve sheath tumors in a neurofibromatosis type 1 mouse model. Cancer Research 66, 62–68. #' @source Karlyne Reilly, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, [email protected]
link{gutlength} link{iron}, link{myocard},
link{ovar}, link{trout}
data(nf1) library(qtl) plot(nf1)data(nf1) library(qtl) plot(nf1)
Data on ovariole number in a backcross between D. simulans and D. sechellia; the majority of individuals were selected to be recombinant in the region of a putative QTL on chromosome 3.
ovarovar
An object of class cross. See qtl::read.cross()
for details.
The data come from an interspecific Drosophila backcross. D.
simulans was crossed to D. sechellia, and the hybrid
was crossed back to D. simulans.
The phenotype of interest was ovariole number in females (a measure of
fitness). Phenotypes on1 and on2 are the ovariole counts in
the left and right gonads. The phenotype onm is the average of the
two counts; for many individuals, the ovariole count for one of two gonads
was missing, and so onm is missing.
In an initial cross of 402 individuals, 383 had complete phenotype data. Initial genotyping focused on 94 individuals with extreme phenotype.
To increase the resolution of a major QTL identified on chromosome 3, a second cross of approximately 7000 flies was performed, though only 1050 individuals showing a recombination event between two morphological markers, st (bright red eyes) and e (dark brown body), were phenotyped and genotyped; 1038 had complete phenotype data. The aim was to oversample recombinants of the region of the QTL.
There are genotype data for 24 markers on 3 chromosomes. (The fourth chromosome had one marker, but showed no effect and is not included in these data.)
The phenotype cross indicates whether an individual came from the
first or second cross.
Alleles "I" and "E" refer to D. simulans and D.
sechellia, respectively.
Virginie Orgogozo, Department of Ecology and Evolutionary Biology, Princeton University, [email protected]
Orgogozo, V., Broman, K. W. and Stern, D. L. (2006) High-resolution QTL mapping reveals sign epistasis controlling ovariole number between two Drosophila species. Genetics 173, 197–205.
link{gutlength}, link{iron}, link{myocard},
link{nf1}, link{trout}
data(ovar) library(qtl) plot(ovar)data(ovar) library(qtl) plot(ovar)
Data from doubled haploid individuals derived from a cross between Oregon State University (OSU) and Clearwater (CW) River rainbow trout clonal lines.
trouttrout
An object of class cross. See qtl::read.cross()
for details.
Doubled haploid individuals were produced from a cross between Oregon State
University (OSU) and Clearwater (CW) river rainbow trout (Oncorhynchus
mykiss) clonal lines. Eggs from one of eight outbred females, two from
Troutlodge (TL) and six from Spokane (SP), were irradiated to destroy
maternal nuclear DNA and fertilized with sperm from a single
male. The first embryonic cleavage was blocked by heat shock to restore
diploidy. There are a total of 554 individuals, with between 8 and 168
individuals from each of the eight females.
The primary phenotype is time to hatch (tth). An additional
"phenotype", female, indicates maternal cytoplasmic environment (the
source of the egg).
There are genotype data on 171 markers on 28 linkage groups. The linkage groups are named as in Nichols et al. (2002), though a pair of markers are assigned to linkage group "un", as they don't connect to any of the linkage groups in Nichols et al. (2002).
Note that the data have cross type "dh" (for doubled haploids); in
R/qtl they are treated just like a backcross, except that genotypes are
referred to as the homozygotes.
Krista M. Nichols, Department of Biological Sciences, Purdue University, [email protected]
Nichols, K. M., Broman, K. W., Sundin, K., Young, J. M., Wheeler, P. A. and Thorgaard, G. H. (2007) Quantitative trait loci by maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss. Genetics 175, 335–347.
Nichols, K. M., Young, W. P., Danzmann, R. G., Robison, B. D., Rexroad, C., Noakes, M., Phillips, R. B., Bentzen, P., Spies, I., Knudsen, K., Allendorf, F. W., Cunningham, B. M., Brunelli, J., Zhang, H., Ristow, S., Drew, R., Brown, K. H., Wheeler, P. A. and Thrgaard, G. H. (2002) A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Animal Genetics 34, 102–115.
link{gutlength}, link{iron}, link{myocard},
link{nf1}, link{ovar}
data(trout) library(qtl) plot(trout)data(trout) library(qtl) plot(trout)