Description
Hi,
I'm not sure about how to use the GetEEJunct and PlotRelDistDistribution funtions.
I test this using the system file miCLIP_m6A_Linder2015_hg38.bed and bsRNAseq_m5C_Squires2012_hg38.bed. And the transcriptome data was downloaded from https://drive.google.com/file/d/0B5_hfxBdKWHRVlBCTUlSazJfaWs/view
Codes:
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("AnnotationDbi", "beanplot", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "gplots", "RSQLite", "rtracklayer"))
biocLite(c("BSgenome.Hsapiens.UCSC.hg38", "org.Hs.eg.db"))
if (!require("devtools")) install.packages("devtools"); devtools::install_github("mevers/RNAModR", build_vignettes = FALSE)
Load the library.
library(RNAModR)
library(RMariaDB)
Build reference transcriptome.
This might take a few minutes.
#BuildTx("hg38")
bedFile <- system.file("extdata", "miCLIP_m6A_Linder2015_hg38.bed", package = "RNAModR")
sites <- ReadBED(bedFile)
posSites <- SmartMap(sites , id= "m6A" ,refGenome = "hg38" )
bedFile <- system.file("extdata",
"bsRNAseq_m5C_Squires2012_hg38.bed",
package = "RNAModR")
sites <- ReadBED(bedFile)
m5Csites <- SmartMap(sites, id= "m5C" ,refGenome = "hg38" )
Error:
PlotRelDistDistribution(posSites,miRNA)
Error: gr1 is not an object of type GRangesList.
junction <- GetEEJunct(refGenome = "hg38", filter = "CDS")
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘psetdiff’ for signature ‘"CompressedGRangesList", "GRangesList"’
Please have a look. Thank you.