fCCAC-package {fCCAC} | R Documentation

## functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

### Description

An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).

### Details

Package: | fCCAC
Type: | Package
Version: | 1.19.3
Date: | 2021-08-25
License: | Artistic-2.0
LazyLoad: | yes

### Author(s)

Pedro Madrigal,

Maintainer: Pedro Madrigal pmadrigal@ebi.ac.uk

### References

Madrigal P (2016) fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets. Bioinformatics: http://doi.org/10.1093/bioinformatics/btw724.

### Examples

    ## 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" )
            ti <- "H3K4me3 peaks"

            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)

            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)
        }

[Package fCCAC version 1.20.0 Index]