 Extending genomation to work with pairedend BAM files
 Accelerate functions responsible for reading genomic files
 Parallelizing data processing in ScoreMatrixList
 Arithmetic, indicator and logic operations as well as subsetting work on ScoreMatrix objects

Improvements and new arguments in visualization functions
 Faster heatmaps
 New clustering possibilities in heatmaps: “clustfun” argument in multiHeatMatrix
 Defining which matrices are used for clustering: “clust.matrix” in multiHeatMatrix
 Central tendencies in line plots: centralTend in plotMeta
 Smoothing central tendency: smoothfun in plotMeta
 Plotting dispersion around central lines in line plots: dispersion in plotMeta
 Calculating scores that correspond to kmer or PWM matrix occurence: patternMatrix function
 Integration with Travis CI for autotesting
Genomation is an R package to summarize, annotate and visualize genomic intervals. It contains a collection of tools for visualizing and analyzing genomewide data sets, i.e. RNAseq, bisulfite sequencing or chromatinimmunoprecipitation followed by sequencing (ChIPseq) data.
Recently we added new features to genomation and here we present them on example of binding profiles of 6 transcription factors around the CTCF binding sites derived from ChIPseq. All new functionalities are available in the latest version of genomation that can be found on its github website.
# install the package from github
library(devtools)
install_github("BIMSBbioinfo/genomation",build_vignettes=FALSE)
Extending genomation to work with pairedend BAM files
Genomation can work with pairedend BAM files. Mates from reads are treated as fragments (they are stitched together).
library(genomation)
genomationDataPath = system.file('extdata',package='genomationData')
bam.files = list.files(genomationDataPath, full.names=TRUE, pattern='bam$')
bam.files = bam.files[!grepl('Cage', bam.files)]
Accelerate functions responsible for reading genomic files
This is achived by using readr::read_delim function to read genomic files instead of read.table. Additionally if skip=“auto” argument is provided in readGeneric_or track.line=“auto” in other functions that read genomic files, e.g. _readBroadPeak then UCSC header is detected (and first track).
library(GenomicRanges)
ctcf.peaks = readBroadPeak(file.path(genomationDataPath,
'wgEncodeBroadHistoneH1hescCtcfStdPk.broadPeak.gz'))
ctcf.peaks = ctcf.peaks[seqnames(ctcf.peaks) == 'chr21']
ctcf.peaks = ctcf.peaks[order(ctcf.peaks$signalValue)]
ctcf.peaks = resize(ctcf.peaks, width=1000, fix='center')
Parallelizing data processing in ScoreMatrixList
We use ScoreMatrixList function to extract coverage values of all transcription factors around ChIPseq peaks. ScoreMatrixList was improved by adding new argument cores that indicates number of cores to be used at the same time (by using parallel:mclapply).
sml = ScoreMatrixList(bam.files, ctcf.peaks, bin.num=50, type='bam', cores=2)
# descriptions of file that contain info. about transcription factors
sampleInfo = read.table(system.file('extdata/SamplesInfo.txt',
package='genomationData'),header=TRUE, sep='\t')
names(sml) = sampleInfo$sampleName[match(names(sml),sampleInfo$fileName)]
Arithmetic, indicator and logic operations as well as subsetting work on score matrices
Arithmetic, indicator and logic operations work on ScoreMatrix, ScoreMatrixBin and ScoreMatrixList
objects, e.i.:
Arith: “+”, “”, “*”, “^{”,} “%%”, “%/%”, “/”
Compare: “==”, “>”, “<”, “!=”, “<=”, “>=”
Logic: “&”, “”
sml1 = sml * 100
sml1
## scoreMatrixlist of length:5
##
## 1. scoreMatrix with dims: 1681 50
## 2. scoreMatrix with dims: 1681 50
## 3. scoreMatrix with dims: 1681 50
## 4. scoreMatrix with dims: 1681 50
## 5. scoreMatrix with dims: 1681 50
Subsetting:
sml[[6]] = sml[[1]]
sml
## scoreMatrixlist of length:6
##
## 1. scoreMatrix with dims: 1681 50
## 2. scoreMatrix with dims: 1681 50
## 3. scoreMatrix with dims: 1681 50
## 4. scoreMatrix with dims: 1681 50
## 5. scoreMatrix with dims: 1681 50
## 6. scoreMatrix with dims: 1681 50
sml[[6]] < NULL
Improvements and new arguments in visualization functions
Due to large signal scale of rows of each element in the ScoreMatrixList we scale them.
sml.scaled = scaleScoreMatrixList(sml)
Faster heatmaps
HeatMatrix and multiHeatMatrix function works faster by faster assigning colors. Heatmap profile of scaled coverage shows a colocalization of Ctcf, Rad21 and Znf143.
multiHeatMatrix(sml.scaled, xcoords=c(500, 500))
New clustering possibilities in heatmaps: “clustfun” argument in multiHeatMatrix
clustfun allow to add more clustering functions and integrate them with the heatmap function multiHeatMatrix. It has to be a function that returns a vector of integers indicating the cluster to which each point is allocated. Previous version of multiHeatMatrix could cluster rows of heatmaps using only kmeans algorithm.
# kmeans algorithm with 2 clusters
cl1 < function(x) kmeans(x, centers=2)$cluster
multiHeatMatrix(sml.scaled, xcoords=c(500, 500), clustfun = cl1)
# hierarchical clustering with Ward's method for agglomeration into 2 clusters
cl2 < function(x) cutree(hclust(dist(x), method="ward"), k=2)
multiHeatMatrix(sml.scaled, xcoords=c(500, 500), clustfun = cl2)
## The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Defining which matrices are used for clustering: “clust.matrix” in multiHeatMatrix
clust.matrix argument indicates which matrices are used for clustering. It can be a numerical vector of indexes of matrices or a character vector of names of the ‘ScoreMatrix’ objects in 'ScoreMatrixList'. Matrices that are not in clust.matrix are ordered according to the result of the clustering algorithm. By default all matrices are clustered.
multiHeatMatrix(sml.scaled, xcoords=c(500, 500), clustfun = cl1, clust.matrix = 1)
Central tendencies in line plots: centralTend in plotMeta
We extended visualization capabilities for metaplots. plotMeta function can plot not only mean, but also median as central tendency and it can be set up using centralTend argument. Previously user could plot only mean.
plotMeta(mat=sml.scaled, profile.names=names(sml.scaled),
xcoords=c(500, 500),
winsorize=c(0,99),
centralTend="mean")
Smoothing central tendency: smoothfun in plotMeta
We added smoothfun argument to smooth central tendency as well as dispersion bands around it which is shown in the next figure. Smoothfun has to be a function that returns a list that contains a vector of y coordinates (vector named '$y').
plotMeta(mat=sml.scaled, profile.names=names(sml.scaled),
xcoords=c(500, 500),
winsorize=c(0,99),
centralTend="mean",
smoothfun=function(x) stats::smooth.spline(x, spar=0.5))
Plotting dispersion around central lines in line plots: dispersion in plotMeta
We added new argument dispersion to plotMeta that shows dispersion bands around centralTend. It can take one of the arguments:
 “se” shows standard error of the mean and 95 percent confidence interval for the mean
 “sd” shows standard deviation and 2*(standard deviation)
 “IQR” shows 1st and 3rd quartile and confidence interval around the median based on the median +/ 1.57 * IQR/sqrt(n) (notches)
plotMeta(mat=sml, profile.names=names(sml),
xcoords=c(500, 500),
winsorize=c(0,99),
centralTend="mean",
smoothfun=function(x) stats::smooth.spline(x, spar=0.5),
dispersion="se", lwd=4)
Calculating scores that correspond to kmer or PWM matrix occurence: patternMatrix function
We added new function patternMatrix that calculates kmer and PWM occurrences over predefined equal width windows. If one pattern (character of length 1 or PWM matrix) is given then it returns ScoreMatrix, if more than one character ot list of PWM matrices then ScoreMatrixList. It finds either positions of pattern hits above a specified threshold and creates score matrix filled with 1 (presence of pattern) and 0 (its absence) or matrix with score themselves. windows can be a DNAStringList object or GRanges object (but then genome argument has to be provided, a BSgenome object).
#ctcf motif from the JASPAR database
ctcf.pfm = matrix(as.integer(c(87,167,281,56,8,744,40,107,851,5,333,54,12,56,104,372,82,117,402,
291,145,49,800,903,13,528,433,11,0,3,12,0,8,733,13,482,322,181,
76,414,449,21,0,65,334,48,32,903,566,504,890,775,5,507,307,73,266,
459,187,134,36,2,91,11,324,18,3,9,341,8,71,67,17,37,396,59)),
ncol=19,byrow=TRUE)
rownames(ctcf.pfm) < c("A","C","G","T")
prior.params = c(A=0.25, C=0.25, G=0.25, T=0.25)
priorProbs = prior.params/sum(prior.params)
postProbs = t( t(ctcf.pfm + prior.params)/(colSums(ctcf.pfm)+sum(prior.params)) )
ctcf.pwm = Biostrings::unitScale(log2(postProbs/priorProbs))
library(BSgenome.Hsapiens.UCSC.hg19)
hg19 = BSgenome.Hsapiens.UCSC.hg19
p = patternMatrix(pattern=ctcf.pwm, windows=ctcf.peaks, genome=hg19, min.score=0.8)
Visualization of the patternMatrix patternMatrix (here as ScoreMatrix object) can be visualized using i.e. heatMatrix, heatMeta or plotMeta functions.
heatMatrix(p, xcoords=c(500, 500), main="CTCF motif")
plotMeta(mat=p, xcoords=c(500, 500), smoothfun=function(x) stats::lowess(x, f = 1/10),
line.col="red", main="ctcf motif")
Integration with Travis CI for autotesting
Recently we integrated genomation with Travis CI. It allows users to see current status
of the package which is updated during every change of the package. Travis
automatically runs R CMD CHECK and reports it. Shields shown below are on the genomation github site:
https://github.com/BIMSBbioinfo/genomation
Status
# <br />
sessionInfo()
## R version 3.2.2 (20150814)
## Platform: x86_64appledarwin13.4.0 (64bit)
## Running under: OS X 10.10.5 (Yosemite)
##
## locale:
## [1] en_US.UTF8/en_US.UTF8/en_US.UTF8/C/en_US.UTF8/en_US.UTF8
##
## attached base packages:
## [1] stats4 parallel grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.3
## [3] rtracklayer_1.28.10 Biostrings_2.36.4
## [5] XVector_0.8.0 GenomicRanges_1.20.8
## [7] GenomeInfoDb_1.4.3 IRanges_2.2.9
## [9] S4Vectors_0.6.6 BiocGenerics_0.14.0
## [11] genomation_1.1.27 BiocInstaller_1.18.5
## [13] devtools_1.9.1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.1 formatR_1.2.1
## [3] futile.logger_1.4.1 plyr_1.8.3
## [5] bitops_1.06 futile.options_1.0.0
## [7] tools_3.2.2 zlibbioc_1.14.0
## [9] digest_0.6.8 gridBase_0.47
## [11] evaluate_0.8 memoise_0.2.1
## [13] gtable_0.1.2 curl_0.9.3
## [15] yaml_2.1.13 proto_0.310
## [17] httr_1.0.0 stringr_1.0.0
## [19] knitr_1.11 data.table_1.9.6
## [21] impute_1.42.0 R6_2.1.1
## [23] plotrix_3.512 XML_3.981.3
## [25] BiocParallel_1.2.22 seqPattern_1.0.1
## [27] rmarkdown_0.8.1 readr_0.1.1
## [29] reshape2_1.4.1 ggplot2_1.0.1
## [31] lambda.r_1.1.7 magrittr_1.5
## [33] matrixStats_0.14.2 MASS_7.344
## [35] scales_0.3.0 Rsamtools_1.20.5
## [37] htmltools_0.2.6 GenomicAlignments_1.4.2
## [39] colorspace_1.26 KernSmooth_2.2315
## [41] stringi_0.55 munsell_0.4.2
## [43] RCurl_1.954.7 chron_2.347
## [45] markdown_0.7.7