I am trying to run the MeQA tool and it has integrated R package MEDIPS. I have installed all the dependencies the whole pipeline runs.
But When i checked the pipeline the methylation file is not genrating by MEDIPS. So the further results are not coming.
Below is My query
The MEDIPS.readAlignedSequences() command of MEDIP is not running . I have checked my libraries are properly installed (MEDIPS and BSgenome.Hsapiens.UCSC.hg19 ).
if(is.element('MEDIPS', installed.packages()[,1]) == FALSE)
{
source("http://www.bioconductor.org/biocLite.R")
biocLite("MEDIPS")
}
library(MEDIPS)
if(is.element('BSgenome.Hsapiens.UCSC.hg19', installed.packages()[,1]) == FALSE)
{
source("http://www.bioconductor.org/biocLite.R")
biocLite("BSgenome.Hsapiens.UCSC.hg19")
}
library("BSgenome.Hsapiens.UCSC.hg19")
fileBed="demo//demo.sorted.bed"
CONTROL.SET = MEDIPS.readAlignedSequences(BSgenome = "BSgenome.Hsapiens.UCSC.hg19",file = fileBed, numrows = 498020)
CONTROL.SET = MEDIPS.genomeVector(data = CONTROL.SET, bin_size = 50,extend = 400)
sr.control = MEDIPS.saturationAnalysis(data = CONTROL.SET, bin_size = 50, extend = 400, no_iterations = 10, no_random_iterations = 1)
jpeg(filename="demo/demo-saturation.jpeg",quality=100)
MEDIPS.plotSaturation(sr.control)
The Error message which i am getting is below.
{
Warning message:
'MEDIPS.readAlignedSequences' is deprecated.
Use 'MEDIPS.createSet' instead.
See help("Deprecated")
Warning message:
'MEDIPS.genomeVector' is deprecated.
Use 'MEDIPS.createSet' instead.
See help("Deprecated")
Warning message:
'MEDIPS.saturationAnalysis' is deprecated.
Use 'MEDIPS.saturation' instead.
See help("Deprecated")
Error in .External2(C_X11, paste("jpeg::", quality, ":", filename, sep = ""), :
unable to start device JPEG
Calls: jpeg
In addition: Warning message:
In jpeg(filename = "demo/demo-saturation.jpeg", quality = 100) :
could not open JPEG file 'demo/demo-saturation.jpeg'
Execution halted
}
Before this every thing is working fine. Please let me Know how to solve this Query. MEDIPS tool is integrated with MeQA pipeline so the process is not working properly. So what should be done to resolve this.
Thank You.
