| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: scmeth |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Functions to conduct quality control analysis in methylation data |
| 4 |
-Version: 0.99.21 |
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| 4 |
+Version: 0.99.22 |
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| 5 | 5 |
Author: Divy Kangeyan <[email protected]> |
| 6 | 6 |
Maintainer: Divy Kangeyan <[email protected]> |
| 7 | 7 |
Depends: R (>= 3.5.0) |
| ... | ... |
@@ -19,18 +19,15 @@ |
| 19 | 19 |
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| 20 | 20 |
cpgDensity <- function(bs,organism,windowLength=1000){
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| 21 | 21 |
|
| 22 |
- cov <- bsseq::getCoverage(bs) |
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| 23 |
- gr <- GenomicRanges::granges(bs) |
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| 24 | 22 |
#GenomeInfoDb::seqlevelsStyle(gr) <- GenomeInfoDb::seqlevelsStyle(organism)[1] |
| 25 |
- |
|
| 26 | 23 |
cov <- bsseq::getCoverage(bs) |
| 27 | 24 |
gr <- GenomicRanges::granges(bs) |
| 28 | 25 |
cpg <- Biostrings::DNAString("CG")
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| 29 | 26 |
cpg_gr <- Biostrings::vmatchPattern(cpg, Hsapiens) |
| 30 | 27 |
cpg_gr <- GenomeInfoDb::keepStandardChromosomes(cpg_gr, pruning.mode= "coarse") |
| 31 | 28 |
|
| 32 |
- r_cpg_gr<-GenomicRanges::resize(cpg_gr,width=1000,fix='center') |
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| 33 |
- cpgd<-GenomicRanges::countOverlaps(gr,r_cpg_gr) |
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| 29 |
+ r_cpg_gr <- GenomicRanges::resize(cpg_gr,width=1000,fix='center') |
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| 30 |
+ cpgd <- GenomicRanges::countOverlaps(gr,r_cpg_gr) |
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| 34 | 31 |
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| 35 | 32 |
#cpgd <- Repitools::cpgDensityCalc(gr, organism, window = windowLength) |
| 36 | 33 |
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