Entering edit mode
13 months ago
melissachuaphd
•
0
I want to plot the EnrichedHeatmap using the GenomicRanges of my CNA data. The normalizeToMatrix function returned mat1, which is filled with 0, resulting in Error: You should have at least two distinct break values. when I try to plot it.
library(EnrichedHeatmap)
library(GenomicRanges)
library(data.table)
library(ChIPseeker)
library(tibble)
library(AnnotationHub)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
hub <- AnnotationHub()
hub <- subset(hub, species == "Homo sapiens")
# Gene GRanges
kirp.seg <- kipan.seg[kipan.seg$Sample %in% colnames(exp),]
colnames(kirp.seg) <- c("sample","chrom","start","end")
genes <- makeGRangesFromDataFrame(kirp.seg, keep.extra.columns=TRUE)
# TSS
tss <- promoters(genes, upstream = 2000, downstream = 2000)
# H3K27me3
H3K27me3.query <- query(hub, c("H3K27me3","hg19", "EpigenomeRoadMap", "broadPeak", "chip", "consolidated", "Kidney"))
H3K27me3 <- H3K27me3.query[["AH29489"]]
The mat1 dataframe seems to be filled with 0s, which results in the following error.
mat1 = normalizeToMatrix(H3K4me3, tss, extend = 100000)
EnrichedHeatmap(mat1, name="H3K4me3", col = c("white","red"))
Traceback:
Error: You should have at least two distinct break values.
Data:
> genes
GRanges object with 83715 ranges and 1 metadata column:
seqnames ranges strand | sample
<Rle> <IRanges> <Rle> | <character>
546793 1 61735-72768916 * | TCGA.2K.A9WE.01A
546794 1 72768936-72788725 * | TCGA.2K.A9WE.01A
546795 1 72788844-72811148 * | TCGA.2K.A9WE.01A
546796 1 72811904-75269284 * | TCGA.2K.A9WE.01A
546797 1 75271072-75273866 * | TCGA.2K.A9WE.01A
... ... ... ... . ...
847097 24 2650438-9633865 * | TCGA.Y8.A8S1.01A
847098 24 9648550-9648739 * | TCGA.Y8.A8S1.01A
847099 24 9651430-22214505 * | TCGA.Y8.A8S1.01A
847100 24 22216828-22489357 * | TCGA.Y8.A8S1.01A
847101 24 22514968-59018259 * | TCGA.Y8.A8S1.01A
-------
seqinfo: 24 sequences from an unspecified genome; no seqlengths
