Hi,
I am using ChIPpeakAnno package to annotate the peaks with the gene name of their nearest TSS called by MACS2 from my ChIPseq data. The package annotates them perfectly, but I am getting a lots of LRG symbols in addition to Ensembl ID. Although, It's quite easy to convert the LRG symbols to their corresponding HGNC gene symbol from this browser (https://www.lrg-sequence.org/search/?), but I am looking for ways to avoid getting the LRG symbols.
Following is the R code I am using to annotate the chippeak narrowPeak file.
library(ChIPpeakAnno)
library(data.table)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(EnsDb.Hsapiens.v86)
library(dplyr)
gr1 <- toGRanges("HepG2-5FU_TP53_vs_Input_ChIPseq_peaks.narrowPeak", format = "narrowPeak", header = FALSE)
annotation<- toGRanges(EnsDb.Hsapiens.v86, feature = "gene")
annotated_chippeaks <- annotatePeakInBatch(gr1, annotation, featureType = "TSS")
output_file <- "annotated_peaks.tsv"
write.table(annotated_chippeaks, file = output_file, sep = "\t", quote = FALSE, row.names = FALSE)
I would be grateful if someone helps me to omit the LRG symbols from my result. Thank you
Note: Some of the peaks annotated with LRG symbols are also annotated with ensembl IDs. It's easy to remove the duplicated one. But most of them are only annotated with LRG_IDS. For a long list of genes, it takes quite a long time to annotate the LRG symbols manually.
sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Kiev tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] devtools_2.4.5 usethis_2.2.2
loaded via a namespace (and not attached):
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[85] htmltools_0.5.7 GenomeInfoDbData_1.2.11 R6_2.5.1
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[100] xfun_0.41 MatrixGenerics_1.14.0 fs_1.6.3
[103] pkgconfig_2.0.3
