16 |
17 | `LDheatmap()` is used to produce a graphical display, as a heat map, of pairwise linkage disequilibrium (LD)
18 | measurements for SNPs.
19 | The heat map is a false color image in the upper-left
20 | diagonal of a square plot. A line parallel to
21 | the diagonal of the image indicating
22 | the physical or genetic map positions of the SNPs
23 | may be added, along
24 | with text reporting the total length of the genomic
25 | region considered. Users may also display the heatmap
26 | "flipped" below a horizontal line indicating the map
27 | positions of the SNPs. In this orientation,
28 | tracks may be added above the genetic map.
29 |
30 | ## Installation
31 |
32 | ```{r,eval=FALSE}
33 | # Install the latest release version from CRAN and the
34 | # imported/suggested BioConductor packages with
35 | install.packages("LDheatmap")
36 | source("https://bioconductor.org/biocLite.R")
37 | biocLite(c("snpStats","rtracklayer","GenomicRanges","GenomInfoDb","IRanges"))
38 |
39 | # Install the latest development version from GitHub with
40 | devtools::install_github("SFUStatgen/LDheatmap")
41 | ```
42 |
43 |
44 | ## Homepage
45 |
46 | https://sfustatgen.github.io/LDheatmap/index.html
47 |
48 |
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/man/CEUSNP.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/CEUDataRd.R
3 | \docType{data}
4 | \name{CEUSNP}
5 | \alias{CEUSNP}
6 | \alias{CEUDist}
7 | \alias{hapmapCEU}
8 | \title{Example data set for LDheatmap}
9 | \format{
10 | CEUSNP: A dataframe of SNP genotypes.
11 | Each row represents an individual.
12 | Each column represents a SNP.
13 |
14 | CEUDist: A vector of integers, representing SNP physical map locations on the chromosome.
15 | }
16 | \source{
17 | International HapMap Project \url{ftp://ftp.ncbi.nlm.nih.gov/hapmap/}
18 | }
19 | \usage{
20 | data(CEUSNP); data(CEUDist)
21 | }
22 | \description{
23 | CEUSNP: Genotypes on 15 SNPs for 60 people
24 |
25 | CEUDist: Physical map positions of the 15 SNPs in CEUSNP
26 | }
27 | \details{
28 | Data on SNPs with minor allele frequency greater
29 | than 5\% from a 9kb region of chromosome 7 (base positions 126273659
30 | through 126282556 from release 7 of the International HapMap Project).
31 | Genotypes from 30 parent-offspring trios (both
32 | parents, one offspring) were obtained.
33 | The 30 trios are taken from the so-called CEPH families, a set of
34 | multi-generational families from Utah with ancestry from northern and
35 | western Europe. From this set of 90 people, 60 parents were extracted.
36 | }
37 | \examples{
38 | data(CEUData)
39 | }
40 | \references{
41 | The International HapMap Consortium. A haplotype map of
42 | the human genome. Nature 437, 1299-1320. 2005.
43 | }
44 | \keyword{datasets}
45 |
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/man/recombRate.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/recombRate.R
3 | \name{recombRate}
4 | \alias{recombRate}
5 | \title{Produce recombination rate plot.}
6 | \usage{
7 | recombRate(minRange, maxRange, chromosome, genome = "hg19", vp = viewport(x = 0,
8 | y = 0.99, height = 0.04, just = c("left", "top")), view = "dense")
9 | }
10 | \arguments{
11 | \item{minRange}{The sequence minimum range in base pairs.}
12 |
13 | \item{maxRange}{The sequence maximum range in base pairs.}
14 |
15 | \item{chromosome}{A character string identifying the chromosome.}
16 |
17 | \item{genome}{The genome assembly to use. The default is hg19, the most recent human genome assembly on
18 | the UCSC genome browser.}
19 |
20 | \item{vp}{A \code{viewport}.}
21 |
22 | \item{view}{Display mode. Possible values are \code{"dense"} (the default), \code{"squish"},
23 | \code{"pack"} and \code{"full"}.}
24 | }
25 | \value{
26 | A \code{grob} representing recombination rates.
27 | }
28 | \description{
29 | Plot average rates of recombination from the deCODE genetic map for a specified genetic sequence.
30 | }
31 | \examples{
32 | \donttest{
33 | grid::grid.newpage()
34 | recombRate(129000000, 140000000, "chr7", "hg18")
35 | grid::grid.newpage()
36 | grid::pushViewport(grid::viewport(width=0.8, x=0.2, just="left"))
37 | recombRate(129000000, 140000000, "chr7", "hg18", view="full")
38 | grid::popViewport()
39 | }
40 | }
41 | \references{
42 | \url{http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=recombRate}
43 | }
44 | \author{
45 | Sigal Blay
53 |
54 |
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127 |
128 | Articles
126 |
129 |
136 | All vignettes
130 | 131 | 132 |-
133 |
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56 |
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/data-raw/hapmapCEU.txt:
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1 | "rs4615512" "rs2283089" "rs1894731" "rs2283092" "rs2283093" "rs6978939" "rs6979287" "rs6979572" "rs2283094" "rs2283095" "rs6467111" "rs1111183" "rs2237789" "rs2299531" "rs2299532"
2 | "distance" "126273659" "126274467" "126275007" "126275550" "126275720" "126276105" "126276310" "126276415" "126276827" "126276946" "126279350" "126281163" "126281542" "126282535" "126282556"
3 | "1" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
4 | "2" "T/C" "C/T" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
5 | "3" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
6 | "4" "NA" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/T" "C/T" "C/C" "C/C" "A/G" "NA" "A/A"
7 | "5" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
8 | "6" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/C" "A/A" "T/T" "A/A"
9 | "7" "NA" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
10 | "8" "T/T" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/C" "C/T" "A/G" "T/C" "A/T"
11 | "9" "C/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/T" "C/C" "A/A" "T/T" "A/A"
12 | "10" "T/T" "C/T" "G/G" "C/C" "C/T" "G/G" "G/G" "T/A" "C/T" "C/T" "C/T" "C/C" "A/G" "NA" "A/A"
13 | "11" "T/T" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/C" "C/T" "A/G" "NA" "A/T"
14 | "12" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
15 | "13" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "C/C" "T/T"
16 | "14" "T/C" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/T" "C/T" "C/C" "C/C" "A/G" "T/T" "A/A"
17 | "15" "T/T" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/T" "C/T" "A/G" "T/C" "A/T"
18 | "16" "C/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "A/A" "T/T" "A/A"
19 | "17" "C/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/T" "C/C" "A/A" "T/T" "A/A"
20 | "18" "T/C" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/T" "C/T" "C/C" "C/C" "A/G" "T/T" "A/A"
21 | "19" "C/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "T/T" "C/C" "A/A" "T/T" "A/A"
22 | "20" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
23 | "21" "NA" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "NA" "T/T"
24 | "22" "T/T" "C/T" "A/G" "T/C" "C/C" "T/G" "T/G" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
25 | "23" "T/C" "T/T" "A/G" "T/C" "C/C" "T/G" "T/G" "T/T" "T/T" "C/C" "T/T" "C/C" "A/A" "T/T" "A/A"
26 | "24" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/C" "A/A" "T/T" "A/A"
27 | "25" "T/T" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/C" "C/T" "A/G" "T/C" "A/T"
28 | "26" "T/T" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/C" "C/T" "A/G" "T/C" "A/T"
29 | "27" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
30 | "28" "T/T" "C/C" "G/G" "C/C" "T/T" "G/G" "G/G" "A/A" "C/C" "T/T" "C/C" "C/C" "G/G" "T/T" "A/A"
31 | "29" "NA" "C/T" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/T" "C/T" "C/T" "C/C" "A/G" "NA" "A/A"
32 | "30" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
33 | "31" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
34 | "32" "C/C" "C/T" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/T" "C/C" "A/A" "T/T" "A/A"
35 | "33" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "C/C" "T/T"
36 | "34" "T/C" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/T" "C/T" "C/T" "C/C" "A/G" "T/T" "A/A"
37 | "35" "T/T" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/C" "C/T" "A/G" "T/C" "A/T"
38 | "36" "T/T" "C/C" "G/G" "C/C" "T/T" "G/G" "G/G" "A/A" "C/C" "T/T" "C/C" "C/C" "G/G" "T/T" "A/A"
39 | "37" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
40 | "38" "C/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "A/A" "T/T" "A/A"
41 | "39" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "C/C" "T/T"
42 | "40" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "C/C" "T/T"
43 | "41" "C/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "A/A" "T/T" "A/A"
44 | "42" "C/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "A/A" "T/T" "A/A"
45 | "43" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
46 | "44" "NA" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
47 | "45" "NA" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/T" "C/C" "A/A" "T/T" "A/A"
48 | "46" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
49 | "47" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "C/C" "T/T"
50 | "48" "T/C" "C/C" "A/G" "T/C" "C/T" "T/G" "G/G" "T/A" "C/T" "C/T" "C/T" "C/C" "A/G" "NA" "A/A"
51 | "49" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
52 | "50" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "C/C" "T/T"
53 | "51" "T/C" "C/T" "A/G" "T/C" "C/C" "T/G" "T/G" "T/T" "T/T" "C/C" "C/T" "C/C" "A/A" "T/T" "A/A"
54 | "52" "NA" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
55 | "53" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/C" "C/T" "A/A" "T/C" "A/T"
56 | "54" "T/C" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
57 | "55" "T/T" "C/T" "A/G" "T/C" "C/C" "T/G" "T/G" "T/T" "C/T" "C/C" "C/T" "C/T" "A/A" "T/C" "A/T"
58 | "56" "C/C" "C/T" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "T/T" "C/C" "C/T" "C/C" "A/A" "T/T" "A/A"
59 | "57" "T/T" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/C" "C/T" "A/G" "T/C" "A/T"
60 | "58" "NA" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/C" "C/T" "C/C" "C/T" "A/G" "NA" "A/T"
61 | "59" "T/T" "C/C" "A/A" "T/T" "C/C" "T/T" "T/T" "T/T" "C/C" "C/C" "C/C" "T/T" "A/A" "C/C" "T/T"
62 | "60" "T/C" "C/C" "A/G" "T/C" "C/T" "T/G" "T/G" "T/A" "C/T" "C/T" "C/T" "C/C" "A/G" "NA" "A/A"
63 |
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/R/LDheatmap.marks.R:
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1 | #' @name LDheatmap.marks
2 | #' @aliases LDheatmap.marks
3 | #' @title Plots a symbol in the centers of cells of the heat map image
4 | #' @description The function \code{LDheatmap.marks()} is used to plot
5 | #'a symbol in the centers of cells representing the
6 | #'pairwise linkage disequilibria of specified pairs of SNPs.
7 | #' @usage LDheatmap.marks(LDheatmap, i, j = NULL, pch = 20, gp=gpar(...), ...)
8 | #' @param LDheatmap An object of class \code{"LDheatmap"}
9 | #'returned by the function \code{\link{LDheatmap}()}.
10 | #' @param i A vector of indices of the first set of SNPs.
11 | #' @param j A vector of indices of the second set of SNPs.
12 | #' @param pch Either an integer value or a single character specifying
13 | #'the symbol to be plotted. See \code{\link[graphics]{points}()}
14 | #'for possible values and their corresponding symbols.
15 | #' @param gp Graphical parameters; See \code{\link[grid]{gpar}()}.
16 | #' @param ... Graphical parameter settings to be passed on to the \code{\link[grid]{gpar}()}
17 | #'function.
18 | #' @return \item{ x }{ The vector of x coordinate(s) of the plotted symbol(s).}
19 | #' \item{ y }{ The vector of y coordinate(s) of the plotted symbol(s). }
20 | #' @details The lengths of the vectors \code{i} and \code{j} must be the same and
21 | #'greater than or equal to 1.
22 | #'If the lengths are greater than 1, the function plots the specified
23 | #'symbol in the centers of the (i\eqn{\mbox{\textasciicircum}}{^}k,
24 | #' j\eqn{\mbox{\textasciicircum}}{^}k)-th cells (for k=1,...K; K =
25 | #' length of the vectors \code{i} and \code{j}), where
26 | #'i\eqn{\mbox{\textasciicircum}}{^}k and
27 | #'j\eqn{\mbox{\textasciicircum}}{^}k are
28 | #'the k-th elements of vectors \code{i} and \code{j}, respectively.
29 | #'For example, if \code{i=c(1,2)} and \code{j=c(3,5)}, \code{LDheatmap()}
30 | #'plots a symbol in the centers of the cells representing pairwise
31 | #'linkage disequilibria between the first and third SNPs and between the
32 | #'second and fifth SNPs in the genome of interest. Note that the order
33 | #'of the sets of indices does not matter; for example,
34 | #'\code{LDheatmap.marks(LDheatmap, i=c(1,2), j=c(3,5))} is equivalent
35 | #'to \code{LDheatmap.marks(LDheatmap, i=c(3,5), j=c(1,2))}.
36 | #' @section Warning: By default, \code{LDheatmap.marks()} finds the viewport to draw on from
37 | #'the \code{LDheatmap} object passed to it as an argument.
38 | #'However, if \code{LDheatmap()} was called with the option \code{pop=TRUE},
39 | #'the resulting \code{LDheatmap} object is not assigned a
40 | #'viewport. In this case, \code{LDheatmap.marks()} assumes
41 | #'the user wishes to highlight in the current viewport.
42 | #'Therefore, if \code{LDheatmap()}
43 | #'has been called with the option \code{pop=TRUE},
44 | #'the user must navigate to the correct viewport
45 | #'before calling \code{LDheatmap.marks()}.
46 | #' @author Nicholas Lewin-Koh
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94 | 95 |GIMAP5CEU.Rd
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105 | SNP genotypes on HapMap founders from the CEU population 101 | for SNPs spanning the GIMAP5 gene.
102 | 103 |data(GIMAP5.CEU)106 | 107 |
Format
108 | 109 |GIMAP5.CEU is a list with two elements: snp.data and snp.support.
110 | snp.data is a snp.matrix
111 | object containing the SNP genotypes. Rows correspond to
112 | subjects and columns correspond to SNPs.
113 | snp.support is a data frame with the following columns:
| [,1] | dbSNPalleles | character | alleles at each SNP |
| [,2] | Assignment | character | same as dbSNPalleles |
| [,3] | Chromosome | character | chromosome (chr7 for all) |
| [,4] | Position | numeric | physical position |
Details
121 | 122 |SNP genotypes from HapMap release 27 123 | for SNPs in a 10KB region spanning 124 | the GIMAP5 gene. Data are on founders from the CEU population, 125 | described as Utah residents with Northern and Western European ancestry 126 | from the CEPH collection. 127 | Only those SNPs with minor allele frequency greater 128 | than 5% in all populations were retained. 129 | The base positions are from NCBI build 36 130 | (UCSC genome hg18).
131 | 132 |Source
133 | 134 |International HapMap Project www.hapmap.org
135 | 136 |References
137 | 138 |The International HapMap Consortium. A haplotype map of 139 | the human genome. Nature 437, 1299-1320. 2005.
140 | 141 |See also
142 | 143 | 144 | 145 | 146 |Examples
147 |150 |require(snpStats) # for the SnpMatrix data structure 148 | data(GIMAP5.CEU) 149 | LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)
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129 | 130 |CEUData.Rd
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140 | CEUSNP: Genotypes on 15 SNPs for 60 people
136 |CEUDist: Physical map positions of the 15 SNPs in CEUSNP
137 | 138 |data(CEUData)141 | 142 |
Format
143 | 144 |CEUSNP: A dataframe of SNP genotypes. 145 | Each row represents an individual. 146 | Each column represents a SNP.
147 |CEUDist: A vector of integers, representing SNP physical map locations on the chromosome.
148 | 149 |Source
150 | 151 |International HapMap Project www.hapmap.org
152 | 153 |Details
154 | 155 |Data on SNPs with minor allele frequency greater 156 | than 5% from a 9kb region of chromosome 7 (base positions 126273659 157 | through 126282556 from release 7 of the International HapMap Project). 158 | Genotypes from 30 parent-offspring trios (both 159 | parents, one offspring) were obtained. 160 | The 30 trios are taken from the so-called CEPH families, a set of 161 | multi-generational families from Utah with ancestry from northern and 162 | western Europe. From this set of 90 people, 60 parents were extracted.
163 | 164 |References
165 | 166 |The International HapMap Consortium. A haplotype map of 167 | the human genome. Nature 437, 1299-1320. 2005.
168 | 169 | 170 |Examples
171 |172 |data(CEUData)
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133 | Add a graphical object to an LDheatmap plot
129 | 130 |LDheatmap.addGrob.Rd
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140 | Add a graphical object to an LDheatmap plot such that the x-axis corresponds 136 | to the physical map on the heatmap.
137 | 138 |LDheatmap.addGrob(LDheatmap, grob, height = 0.2)141 | 142 |
Arguments
143 || LDheatmap | 147 |An object of class LDheatmap. |
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| height | 155 |The height of the viewport in which the grob will be placed. |
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Value
160 | 161 |An object of class LDheatmap given as an argument, with the grob
162 | LDheatmapGrob modified to inclue the new child grob.
See also
165 | 166 | 167 | 168 | 169 |Examples
170 |173 |# Add an empty rectangle frame 171 | data(GIMAP5.CEU) 172 | ll<-LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position,flip=TRUE)
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106 | LDheatmap() is used to produce a graphical display, as a heat map, of pairwise linkage disequilibrium (LD) measurements for SNPs. The heat map is a false color image in the upper-left diagonal of a square plot. A line parallel to the diagonal of the image indicating the physical or genetic map positions of the SNPs may be added, along with text reporting the total length of the genomic region considered. Users may also display the heatmap “flipped” below a horizontal line indicating the map positions of the SNPs. In this orientation, tracks may be added above the genetic map.
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125 | 110 | Installation
111 |# Install the latest release version from CRAN and the
112 | # imported/suggested BioConductor packages with
113 | install.packages("LDheatmap")
114 | source("https://bioconductor.org/biocLite.R")
115 | biocLite(c("snpStats","rtracklayer","GenomicRanges","GenomInfoDb","IRanges"))
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117 | # Install the latest development version from GitHub with
118 | devtools::install_github("SFUStatgen/LDheatmap")
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128 | 129 |recombRate.Rd
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138 | Plot average rates of recombination from the deCODE genetic map for a specified genetic sequence.
135 | 136 |recombRate(minRange, maxRange, chromosome, genome = "hg19", vp = viewport(x = 0, 139 | y = 0.99, height = 0.04, just = c("left", "top")), view = "dense")140 | 141 |
Arguments
142 || minRange | 146 |The sequence minimum range in base pairs. |
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| chromosome | 154 |A character string identifying the chromosome. |
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| genome | 158 |The genome assembly to use. The default is hg19, the most recent human genome assembly on 159 | the UCSC genome browser. |
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173 | 174 |A grob representing recombination rates.
References
177 | 178 |http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=recombRate
179 | 180 | 181 |Examples
182 |# NOT RUN { 183 | grid.newpage() 184 | recombRate(129000000, 140000000, "chr7", "hg18") 185 | grid.newpage() 186 | pushViewport(viewport(width=0.8, x=0.2, just="left")) 187 | recombRate(129000000, 140000000, "chr7", "hg18", view="full") 188 | popViewport() 189 | # }190 |