Description Usage Arguments Value Examples
det_dmsg() This function generates lists of differentially methylated CpG sites and the corresponding genes, as determined by application of methylKit functions.
1 2 3 4 5 6 7 8 9 10 |
mrobj |
A methylKit methylRaw or methylRawList object |
genome_ann |
Genome annotation returned by get_genome_annotation() |
threshold |
Cutoff for percent methylation difference, default threshold = 25.0 |
qvalue |
Cutoff for q-value, default q-value = 0.01 |
mc.cores |
Integer denoting how many cores should be used for parallel diffential methylation calculations |
destrand |
methylKit::unite() parameter; default: FALSE. destrand=TRUE combines CpG methylation calls from both strands. |
outfile1 |
File name to which diff sites are written |
outfile2 |
File name to which diff genes are written |
A list of GRanges objects that contain data on differentially methylated sites and genes with such sites
1 2 3 4 5 6 7 8 9 | mydatf <- system.file("extdata","Am.dat",package="BWASPR")
myparf <- system.file("extdata","Am.par",package="BWASPR")
myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
AmHE <- mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",type="CpGhsm",
mincov=1,assembly="Amel-4.5")
genome_ann <- get_genome_annotation(myfiles$parameters)
meth_diff <- det_dmsg(AmHE,genome_ann,threshold=25.0,qvalue=0.01,mc.cores=4,
outfile1="AmHE-dmsites.txt",
outfile2="AmHE-dmgenes.txt")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.