| Previous changeset 63:2ee6ac5227f1 (2019-04-04) Next changeset 65:9ee05ae14aa5 (2019-05-09) |
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modified:
minfi_dmp.xml |
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| diff -r 2ee6ac5227f1 -r 3d083550977f minfi_dmp.xml --- a/minfi_dmp.xml Thu Apr 04 11:20:23 2019 -0400 +++ b/minfi_dmp.xml Thu Apr 04 11:21:19 2019 -0400 |
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| @@ -29,13 +29,9 @@ tab <- tab[,-(11:14),drop=FALSE] -colnames(tab) <- c("seqname","source","feature","start","end","score","strand", "frame","attributes", "names") - -tab[,"source"] <- NULL +tab <- tab[,c(1,4,5,10)] -tab[,"frame"] <- NULL - -tab[,"attributes"] <- NULL +colnames(tab) <- c('chr','start','end','names') dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar) @@ -43,10 +39,10 @@ data <- merge(dmp, tab, by="names",sort = TRUE) -data <- data[c("seqname","start","end","names","score","strand", "feature","intercept", "f", "pval","qval")] +data <- data[,c(6,7,8,1,4,5)] -write.table(data, file= '$dmp', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t") - ]]> +write.table(data, file= '$dmp', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t") +]]> </configfile> </configfiles> <inputs> @@ -56,13 +52,13 @@ <option value="categorical">categorical</option> <option value="continuous">continuous</option> </param> - <param name="q_cutoff" type="integer" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/> + <param name="q_cutoff" type="float" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/> <param name="variance_shrinkage" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Variance Shrinkage" help="Enable variance shrinkage is recommended when sample sizes are small"/> <param type="data" name="ucsc_genome" format="gtf" label="Genome Table" help="UCSC genome data Methyl450"/> </inputs> <outputs> - <data name="dmp" format="interval" label="Differentially Methylated Positions"/> + <data name="dmp" format="interval" label="Differentially Methylated Positions"/> </outputs> <tests> <test> @@ -80,17 +76,12 @@ The output is an interval file with the following columns: - - seqnames + - chr - start - end - - cpg - names - - score - - strand - - feature - - intercept - - f pval - - qval + - pvalue + - qval ]]></help> <expand macro="citations" /> |