Hi,

I am getting below error while running MEDIPS.CpGenrich function?

Thanks

Gaurav

MEDIPS.CpGenrich(file = "NT/H-CRC-02-NT-5mcS6L001R1001 (paired) trimmed (paired) (Reads).bam", BSgenome = "BSgenome.Hsapiens.NCBI.GRCh38", paired = TRUE, chr.select = c(1:22))

Reading bam alignment H-CRC-02-NT-5mcS6L001R1001 (paired) trimmed (paired) (Reads).bam Selecting 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Total number of imported first mate reads in properly mapped pairs: 25867386 scanBamFlag: isPaired = T, isProperPair=TRUE , hasUnmappedMate=FALSE, isUnmappedQuery = F, isFirstMateRead = T, isSecondMateRead = F Mean insertion size: 173.6452 nt SD of the insertion size: 46.93598 nt Max insertion size: 364 nt Min insertion size: 28 nt Creating GRange Object... Keep at most 1 first mate read(s) mapping to the same genomic location Number of remaining short reads: 25648213 Loading chromosome lengths for BSgenome.Hsapiens.NCBI.GRCh38... Calculating CpG density for given regions...

Error in .restrict_IntegerRanges(x, start, end, drop.ranges.mode, use.names) : invalid 'end' length In addition: There were 11 warnings (use warnings() to see them)

R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] BSgenome.Hsapiens.NCBI.GRCh381.3.1000 MEDIPS1.38.0 Rsamtools2.2.3 BSgenome1.54.0
[5] rtracklayer1.46.0 Biostrings2.54.0 XVector0.26.0 GenomicRanges1.38.0
[9] GenomeInfoDb1.22.0 IRanges2.20.2 S4Vectors0.24.3 BiocGenerics0.32.0

loaded via a namespace (and not attached): [1] Rcpp1.0.3 lattice0.20-40 prettyunits1.1.1 gtools3.8.1 assertthat0.2.1 digest0.6.25
[7] BiocFileCache1.10.2 R62.4.1 RSQLite2.2.0 evaluate0.14 httr1.4.1 pillar1.4.3
[13] zlibbioc1.32.0 rlang0.4.5 progress1.2.2 curl4.3 rstudioapi0.11 blob1.2.1
[19] Matrix1.2-18 preprocessCore1.48.0 rmarkdown2.1 BiocParallel1.20.1 stringr1.4.0 RCurl1.98-1.1
[25] bit1.1-15.2 biomaRt2.42.0 DelayedArray0.12.2 compiler3.6.3 xfun0.12 pkgconfig2.0.3
[31] askpass1.1 htmltools0.4.0 openssl1.4.1 tidyselect1.0.0 SummarizedExperiment1.16.1 tibble2.1.3
[37] GenomeInfoDbData1.2.2 DNAcopy1.60.0 matrixStats0.56.0 XML3.99-0.3 crayon1.3.4 dplyr0.8.5
[43] dbplyr1.4.2 rappdirs0.3.1 GenomicAlignments1.22.1 bitops1.0-6 grid3.6.3 DBI1.1.0
[49] magrittr1.5 stringi1.4.6 vctrs0.2.4 tools3.6.3 bit640.9-7 Biobase2.46.0
[55] glue1.3.2 purrr0.3.3 hms0.5.3 yaml2.2.1 AnnotationDbi1.48.0 BiocManager1.30.10
[61] memoise1.1.0 knitr1.28

Hi Gaurav,

Unfortunately the MEDIPS.CpGenrich() function depends on RangedData, which is not available any more. I have not updated MEDIPS to function without RangedData and will not be able to do so in the near future. Therefore, MEDIPS.CpGenrich() is not available for the time being unless you manage to find an old R/Bioconductor setting where RangedData are still available.

I also would like to stress that we have developed a new package ‘qsea’, which has a much improved method for estimating %methylation from MeDIP-seq data. It also does not have the CG enrichment QC, but is much more flexible in terms of parameter settings etc.

All the best, Lukas

On Mar 13, 2020, at 4:15 PM, gaurav4thareja [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:

Activity on a post you are following on support.bioconductor.orghttps://support.bioconductor.org/

User gaurav4tharejahttps://support.bioconductor.org/u/22977/ wrote Question: MEDIPS - Error in MEDIPS.CpGenrichhttps://support.bioconductor.org/p/129044/:

Hi,

I am getting below error while running MEDIPS.CpGenrich function?

Thanks

Gaurav

MEDIPS.CpGenrich(file = "NT/H-CRC-02-NT-5mcS6L001R1001 (paired) trimmed (paired) (Reads).bam", BSgenome = "BSgenome.Hsapiens.NCBI.GRCh38", paired = TRUE, chr.select = c(1:22))

Reading bam alignment H-CRC-02-NT-5mcS6L001R1001 (paired) trimmed (paired) (Reads).bam Selecting 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Total number of imported first mate reads in properly mapped pairs: 25867386 scanBamFlag: isPaired = T, isProperPair=TRUE , hasUnmappedMate=FALSE, isUnmappedQuery = F, isFirstMateRead = T, isSecondMateRead = F Mean insertion size: 173.6452 nt SD of the insertion size: 46.93598 nt Max insertion size: 364 nt Min insertion size: 28 nt Creating GRange Object... Keep at most 1 first mate read(s) mapping to the same genomic location Number of remaining short reads: 25648213 Loading chromosome lengths for BSgenome.Hsapiens.NCBI.GRCh38... Calculating CpG density for given regions...

Error in .restrict_IntegerRanges(x, start, end, drop.ranges.mode, use.names) : invalid 'end' length In addition: There were 11 warnings (use warnings() to see them)

R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] BSgenome.Hsapiens.NCBI.GRCh381.3.1000 MEDIPS1.38.0 Rsamtools2.2.3 BSgenome1.54.0 [5] rtracklayer1.46.0 Biostrings2.54.0 XVector0.26.0 GenomicRanges1.38.0 [9] GenomeInfoDb1.22.0 IRanges2.20.2 S4Vectors0.24.3 BiocGenerics0.32.0

loaded via a namespace (and not attached): [1] Rcpp1.0.3 lattice0.20-40 prettyunits1.1.1 gtools3.8.1 assertthat0.2.1 digest0.6.25 [7] BiocFileCache1.10.2 R62.4.1 RSQLite2.2.0 evaluate0.14 httr1.4.1 pillar1.4.3 [13] zlibbioc1.32.0 rlang0.4.5 progress1.2.2 curl4.3 rstudioapi0.11 blob1.2.1 [19] Matrix1.2-18 preprocessCore1.48.0 rmarkdown2.1 BiocParallel1.20.1 stringr1.4.0 RCurl1.98-1.1 [25] bit1.1-15.2 biomaRt2.42.0 DelayedArray0.12.2 compiler3.6.3 xfun0.12 pkgconfig2.0.3 [31] askpass1.1 htmltools0.4.0 openssl1.4.1 tidyselect1.0.0 SummarizedExperiment1.16.1 tibble2.1.3 [37] GenomeInfoDbData1.2.2 DNAcopy1.60.0 matrixStats0.56.0 XML3.99-0.3 crayon1.3.4 dplyr0.8.5 [43] dbplyr1.4.2 rappdirs0.3.1 GenomicAlignments1.22.1 bitops1.0-6 grid3.6.3 DBI1.1.0 [49] magrittr1.5 stringi1.4.6 vctrs0.2.4 tools3.6.3 bit640.9-7 Biobase2.46.0 [55] glue1.3.2 purrr0.3.3 hms0.5.3 yaml2.2.1 AnnotationDbi1.48.0 BiocManager1.30.10 [61] memoise1.1.0 knitr1.28