fccac | R Documentation |
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets.
fccac(peaks, bigwigs, labels, splines=10, nbins=100, ncan=5 , tf=c(), main="", bar=NULL, outFiles=FALSE )
peaks |
BED file. Column 1: chr, Column 2: start, Column 3: end (Required). |
bigwigs |
A vector of characters containing the path to bigwigs files. Replicates of the same samples should be entered consecutive one another (Required). |
labels |
IDs for each sample. Replicates should have the same label and be ordered (vector of characters, Required) |
splines |
Number of cubic B-splines used to smooth the data and to estimate the canonical variate weight functions (default: 15) |
nbins |
Integer value representing the number of bins that should be used for each window (default: 100) |
ncan |
Number of canonical components to report in the results. It cannot be higher than number of splines or the number of peaks (default: 15) |
tf |
Plot results involving only this TF or TF-replicate (character). Eg., "SOX2" or "SOX2\_Rep1" (default: empty vector. plot all) |
main |
Title of the plot generated (default: no title) |
bar |
In the barplot, plot only first bar[1] and last bar[2] interactions after ranking by F-value (default: NULL, plots all the combinations). |
outFiles |
If TRUE, the function writes two files in the working directory, fCCAC.pdf and fCCAC.txt (tabulated text-file with results). (default: FALSE) |
Detailed information about the methodology can be found in Madrigal (2016).
The function reports a dataframe with the following columns: pairwise samples, F value, k (order of the first canonical correlation), and value of the first canonical correlation.
Pedro Madrigal, pmadrigal@ebi.ac.uk
Madrigal P (2016) fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets. Bioinformatics: http://doi.org/10.1093/bioinformatics/btw724.
fCCAC-package
## hg19. chr21:40000000-48129895 H3K4me3 data from Bertero et al. (2015) if (.Platform$OS.type == "unix") { owd <- setwd(tempdir()) bigwig1 <- "chr21_H3K4me3_1.bw" bigwig2 <- "chr21_H3K4me3_2.bw" bigwig3 <- "chr21_H3K4me3_3.bw" peakFile <- "chr21_merged_ACT_K4.bed" labels <- c( "H3K4me3", "H3K4me3","H3K4me3" ) r1 <- system.file("extdata", bigwig1, package="fCCAC",mustWork = TRUE) r2 <- system.file("extdata", bigwig2, package="fCCAC",mustWork = TRUE) r3 <- system.file("extdata", bigwig3, package="fCCAC",mustWork = TRUE) r4 <- system.file("extdata", peakFile, package="fCCAC",mustWork = TRUE) ti <- "H3K4me3 peaks" fc <- fccac(bar=NULL, main=ti, peaks=r4, bigwigs=c(r1,r2,r3), labels=labels, splines=15, nbins=100, ncan=15) head(fc) setwd(owd) }
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