GRanges to bed correctly + meth stats , seperate files

.test/comparison/config.yaml

@@ -15,5 +15,5 @@ params:
   qValue: 0.01
   minCov: 4
   minDiff: 0.4
-  context: ["CpG", "CHG", "CHH"]
+  context: ["CG"]
   species: "Malus Domestica"

config/configComparison.yaml

@@ -7,17 +7,13 @@ resources:
     genome: ".test/resources/genome/Malus_domestica_cultivar_Golden_Delicious-chr4.fasta"
   annot: ".test/resources/annot/WT_vs_Meth13-CG.bed" #optional must be "" empty string if not being used
 params:
-  method: bins
-  binSize: 500
-  kernelFunction: triangular
-  test: fisher
-  pseudocountM: 1
-  pseudocountN: 2
-  pValueThreshold: 0.01
-  minCytosinesCount: 1 # default 4 in bins/noise_filter , must be 1 for neighbourhood method
-  minProportionDifference: 0.4
-  minGap: 50
-  minSize: 100
-  minReadsPerCytosine: 4
-  cores: 1
-  context: ["CG", "CHG"]
+  bins: TRUE
+  windowSize: 1000
+  stepSize: 1000
+  test: F # default F, Chisq for overdispersion
+  overdispersion: none # default none, NM for overdispersion
+  qValue: 0.01
+  minCov: 4
+  minDiff: 0.4
+  context: ["CG"]
+  species: "Malus Domestica"

workflow/rules/computeDmrs.smk

@@ -22,10 +22,12 @@ rule compute_methylkit:
 		clustersPdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-clusters.pdf",
 		pcaScreePdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-PCA-screeplot.pdf",
 		pcaPdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-PCA.pdf",
-		hyperMethylation=outdir+"methylkit_results/{id}-{context}/{id}-{context}-HyperMethylated.txt",
-		hypoMethylation=outdir+"methylkit_results/{id}-{context}/{id}-{context}-HypoMethylated.txt",
-		overAllMethylation=outdir+"methylkit_results/{id}-{context}/{id}-{context}-overallMethylation.txt",
-
+		hyperMethylation=outdir+"methylkit_results/{id}-{context}/{id}-{context}-HyperMethylated-stats.txt",
+		hypoMethylation=outdir+"methylkit_results/{id}-{context}/{id}-{context}-HypoMethylated-stats.txt",
+		overAllMethylation=outdir+"methylkit_results/{id}-{context}/{id}-{context}-overallMethylation-stats.txt",
+		hyperMethylationBed=outdir+"methylkit_results/{id}-{context}/{id}-{context}-HyperMethylated.bed",
+		hypoMethylationBed=outdir+"methylkit_results/{id}-{context}/{id}-{context}-HypoMethylated.bed",
+		overAllMethylationBed=outdir+"methylkit_results/{id}-{context}/{id}-{context}-overallMethylation.bed",
 	log:
 		outdir+"methylkit_results/{id}-{context}/{id}-{context}-log.out"
 	conda:

workflow/scripts/methylkit.R

@@ -106,19 +106,34 @@ methDiff=calculateDiffMeth(meth,overdispersion=overdispersion,test=testOverdispe
 
 ### filtering differential methylation ###
 fileTxt<-file(snakemake@output[["hyperMethylation"]])
+hyper <- getMethylDiff(methDiff,difference=minDiff,qvalue=qValue,type="hyper")
 sink(fileTxt)
-getMethylDiff(methDiff,difference=minDiff,qvalue=qValue,type="hyper")
+hyper
 sink()
 close(fileTxt)
 
+my.gr=as(hyper,"GRanges")
+df <- data.frame(my.gr)
+write.table(df, file=snakemake@output[["hyperMethylationBed"]], quote=F, sep="\t", row.names=F, col.names=F)
+
+hypo <- getMethylDiff(methDiff,difference=minDiff,qvalue=qValue,type="hypo")
 fileTxt<-file(snakemake@output[["hypoMethylation"]])
 sink(fileTxt)
-getMethylDiff(methDiff,difference=minDiff,qvalue=qValue,type="hypo")
+hypo 
 sink()
 close(fileTxt)
 
+my.gr=as(hypo,"GRanges")
+df <- data.frame(my.gr)
+write.table(df, file=snakemake@output[["hypoMethylationBed"]], quote=F, sep="\t", row.names=F, col.names=F)
+
+all <- getMethylDiff(methDiff,difference=minDiff,qvalue=qValue)
 fileTxt<-file(snakemake@output[["overAllMethylation"]])
 sink(fileTxt)
-getMethylDiff(methDiff,difference=minDiff,qvalue=qValue)
+all
 sink()
 close(fileTxt)
+
+my.gr=as(all,"GRanges")
+df <- data.frame(my.gr)
+write.table(df, file=snakemake@output[["overAllMethylationBed"]], quote=F, sep="\t", row.names=F, col.names=F)