Integrate Differential Expression Results and Peak Annotation Results of ChIP-seq and ATAC-seq.

DEbCA(
  de.res,
  chip.peak.res,
  atac.peak.res,
  peak.anno.key = c("Promoter", "5' UTR", "3' UTR", "Exon", "Intron", "Downstream",
    "Distal Intergenic", "All"),
  signif = "padj",
  signif.threshold = 0.05,
  l2fc.threshold = 1,
  label.key = NULL,
  merge.key = c("geneId", "ENSEMBL", "SYMBOL")
)

Arguments

de.res	Data frame contains all genes of differential expression analysis.
chip.peak.res	Dataframe contains peak annotation results of ChIP-seq data.
atac.peak.res	Dataframe contains peak annotation results of ATAC-seq data.
peak.anno.key	Peak location, chosen from "Promoter", "5' UTR", "3' UTR", "Exon", "Intron", "Downstream", "Distal Intergenic","All". Default: "Promoter".
signif	Significance criterion. For DESeq2 results, can be chosen from padj, pvalue. For edgeR results, can be chosen from FDR, PValue. Default: padj.
signif.threshold	Significance threshold to get differentially expressed genes. Default: 0.05.
l2fc.threshold	Log2 fold change threshold to get differentially expressed genes. Default: 1.
label.key	Which column to use as label. Default: NULL (use rownames of `deres`).
merge.key	The columns used for merging, chosen from geneId, ENSEMBL, SYMBOL. Default: geneId.

Value

Dataframe contains integrated results. The results will contain eleven categories: UP, DOWN, ChIP, ATAC, UPbChIP, DOWNbChIP UPbATAC, DOWNbATAC, ChIPbATAC, UPbPeak, DOWNbPeak.

Examples

library(DEbPeak)
library(DESeq2)
# ChIP-Seq data
peak.file <- system.file("extdata", "debchip_peaks.bed", package = "DEbPeak")
peak.df <- GetConsensusPeak(peak.file = peak.file)
peak.profile <- PeakProfile(peak.df, species = "Mouse", by = "gene", region.type = "body", nbin = 800)
#> >> preparing promoter regions...	 2023-07-02 17时06分49秒 
#> >> preparing tag matrix...		 2023-07-02 17时06分49秒 
#> >> preparing start_site regions by ... 2023-07-02 17时06分49秒
#> >> preparing tag matrix...  2023-07-02 17时06分49秒 
#> >> generating figure...		 2023-07-02 17时06分58秒 
#> >> done...			 2023-07-02 17时06分58秒 
#> >> binning method is used...2023-07-02 17时06分58秒
#> >> preparing start_site regions by gene... 2023-07-02 17时06分58秒
#> >> preparing tag matrix by binning...  2023-07-02 17时06分58秒 
#> >> Running bootstrapping for tag matrix...		 2023-07-02 17时07分05秒 
#> >> binning method is used...2023-07-02 17时07分05秒
#> >> preparing body regions by gene... 2023-07-02 17时07分05秒
#> >> preparing tag matrix by binning...  2023-07-02 17时07分05秒 
#> >> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-07-02 17时07分05秒
#> >> 1 peaks(0.1536098%), having lengths smaller than 800bp, are filtered... 2023-07-02 17时07分08秒
#> >> Running bootstrapping for tag matrix...		 2023-07-02 17时07分46秒 
peak.anno <- AnnoPeak(
  peak.df = peak.df, species = "Mouse",
  seq.style = "UCSC", up.dist = 20000, down.dist = 20000
)
#> >> preparing features information...		 2023-07-02 17时07分47秒 
#> >> identifying nearest features...		 2023-07-02 17时07分47秒 
#> >> calculating distance from peak to TSS...	 2023-07-02 17时07分48秒 
#> >> assigning genomic annotation...		 2023-07-02 17时07分48秒 
#> >> adding gene annotation...			 2023-07-02 17时07分50秒 
#> 'select()' returned 1:many mapping between keys and columns
#> >> assigning chromosome lengths			 2023-07-02 17时07分50秒 
#> >> done...					 2023-07-02 17时07分50秒 
#> Warning: Removed 6 rows containing non-finite values (`stat_count()`).
# RNA-Seq data
count.file <- system.file("extdata", "debchip_count.txt", package = "DEbPeak")
meta.file <- system.file("extdata", "debchip_meta.txt", package = "DEbPeak")
count.matrix <- read.table(file = count.file, header = TRUE, sep = "\t")
meta.info <- read.table(file = meta.file, header = TRUE)
# create DESeqDataSet object
dds <- DESeq2::DESeqDataSetFromMatrix(
  countData = count.matrix, colData = meta.info,
  design = ~condition
)
#> Warning: some variables in design formula are characters, converting to factors
# set control level
dds$condition <- relevel(dds$condition, ref = "NF")
# conduct differential expressed genes analysis
dds <- DESeq(dds)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
# extract results
dds.results <- results(dds, contrast = c("condition", "RX", "NF"))
dds.results.ordered <- dds.results[order(dds.results$log2FoldChange, decreasing = TRUE), ]
# Integrated with RNA-Seq
debchip.res <- DEbPeak(
  de.res = dds.results.ordered, peak.res = peak.anno[["df"]],
  peak.anno.key = "Promoter", merge.key = "SYMBOL"
)
#> Differential expression analysis with DESeq2!
# ATAC-seq data
atac.peak.file <- system.file("extdata", "debatac_peaks.bed", package = "DEbPeak")
atac.peak.df <- GetConsensusPeak(peak.file = atac.peak.file)
atac.peak.profile <- PeakProfile(atac.peak.df, species = "Mouse", by = "gene", region.type = "body", nbin = 800)
#> >> preparing promoter regions...	 2023-07-02 17时08分00秒 
#> >> preparing tag matrix...		 2023-07-02 17时08分00秒 
#> >> preparing start_site regions by ... 2023-07-02 17时08分00秒
#> >> preparing tag matrix...  2023-07-02 17时08分00秒 
#> >> generating figure...		 2023-07-02 17时08分07秒 
#> >> done...			 2023-07-02 17时08分12秒 
#> >> binning method is used...2023-07-02 17时08分14秒
#> >> preparing start_site regions by gene... 2023-07-02 17时08分14秒
#> >> preparing tag matrix by binning...  2023-07-02 17时08分14秒 
#> >> Running bootstrapping for tag matrix...		 2023-07-02 17时08分58秒 
#> >> binning method is used...2023-07-02 17时08分58秒
#> >> preparing body regions by gene... 2023-07-02 17时08分58秒
#> >> preparing tag matrix by binning...  2023-07-02 17时08分58秒 
#> Warning: GRanges object contains 1 out-of-bound range located on sequence chrX.
#>   Note that ranges located on a sequence whose length is unknown (NA) or
#>   on a circular sequence are not considered out-of-bound (use
#>   seqlengths() and isCircular() to get the lengths and circularity flags
#>   of the underlying sequences). You can use trim() to trim these ranges.
#>   See ?`trim,GenomicRanges-method` for more information.
#> Warning: GRanges object contains 1 out-of-bound range located on sequence chrX.
#>   Note that ranges located on a sequence whose length is unknown (NA) or
#>   on a circular sequence are not considered out-of-bound (use
#>   seqlengths() and isCircular() to get the lengths and circularity flags
#>   of the underlying sequences). You can use trim() to trim these ranges.
#>   See ?`trim,GenomicRanges-method` for more information.
#> >> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-07-02 17时08分58秒
#> >> 16 peaks(0.296077%), having lengths smaller than 800bp, are filtered... 2023-07-02 17时09分04秒
#> >> Running bootstrapping for tag matrix...		 2023-07-02 17时12分02秒 
atac.peak.anno <- AnnoPeak(
  peak.df = atac.peak.df, species = "Mouse",
  seq.style = "UCSC", up.dist = 20000, down.dist = 20000
)
#> >> preparing features information...		 2023-07-02 17时12分03秒 
#> >> identifying nearest features...		 2023-07-02 17时12分03秒 
#> >> calculating distance from peak to TSS...	 2023-07-02 17时12分03秒 
#> >> assigning genomic annotation...		 2023-07-02 17时12分03秒 
#> >> adding gene annotation...			 2023-07-02 17时12分05秒 
#> 'select()' returned 1:many mapping between keys and columns
#> >> assigning chromosome lengths			 2023-07-02 17时12分06秒 
#> >> done...					 2023-07-02 17时12分06秒 
#> Warning: Removed 23 rows containing non-finite values (`stat_count()`).
debpeak.res <- DEbCA(
  de.res = dds.results.ordered, chip.peak.res = peak.anno[["df"]],
  atac.peak.res = atac.peak.anno[["df"]],
  peak.anno.key = "Promoter", merge.key = "SYMBOL"
)
#> Differential expression analysis with DESeq2!