heatmapfCCAC: Heatmap of F values obtained by Canonical Correlation...

In pmb59/fCCAC: functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Heatmap of F values obtained by Canonical Correlation Analysis

Description

Heatmap of F values obtained by Canonical Correlation Analysis. This function can only be used if all pairwise comparisons were computed previously with the function 'fccac', i.e., using "tf=c()".

Usage

  heatmapfCCAC(fc)

Arguments

fc	Output of the function 'fccac'.

Value

Plots a Heatmap of F values using the package 'ComplexHeatmap'.

Author(s)

Pedro Madrigal, [e-mail]

References

Madrigal P (2017) fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets. Bioinformatics: http://doi.org/10.1093/bioinformatics/btw724.

See Also

fccac

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" )

    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)

    heatmapfCCAC(fc)

    setwd(owd)
    
  }

pmb59/fCCAC documentation built on May 31, 2022, 4:38 a.m.