hello,
i am not an expert in R and i am trying to use MEDIPS package for medip-seq data analysis. But i am having this error er=MEDIPS.CpGenrich(file=bam.file.hESCs.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select="chr22", extend=0, shift=0, uniq=1e-3)
Reading bam alignment hESCs.MeDIP.Rep1.chr22.bam Selecting chr22 Total number of imported short reads: 152586 Creating GRange Object... Keep at most 1 read(s) mapping to the same genomic location Number of remaining reads: 150793 Loading chromosome lengths for BSgenome.Hsapiens.UCSC.hg19... 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)
When i checked the warnings, they are all the same following messag : 11: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
Any advices?
Thank you!
My session infos are
Matrix products: default BLAS: /.mounts/labs/awadallalab/modulator/sw/Ubuntu18.04/rstats-3.6/lib/R/lib/libRblas.so LAPACK: /.mounts/labs/awadallalab/modulator/sw/Ubuntu18.04/rstats-3.6/lib/R/lib/libRlapack.so
locale: [1] LCCTYPE=enUS LCNUMERIC=C LCTIME=enUS
[4] LCCOLLATE=enUS LCMONETARY=enUS LCMESSAGES=enUS
[7] LCPAPER=enUS LCNAME=C LCADDRESS=C
[10] LCTELEPHONE=C LCMEASUREMENT=enUS LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] optparse1.6.4 MEDIPSData1.22.0
[3] BSgenome.Hsapiens.UCSC.hg381.4.1 MEDIPS1.38.0
[5] Rsamtools2.2.3 BSgenome.Hsapiens.UCSC.hg191.4.0 [7] BSgenome1.54.0 rtracklayer1.46.0
[9] Biostrings2.54.0 XVector0.26.0
[11] GenomicRanges1.38.0 GenomeInfoDb1.22.0
[13] IRanges2.20.2 S4Vectors0.24.3
[15] BiocGenerics_0.32.0
loaded via a namespace (and not attached): [1] Rcpp1.0.3 lattice0.20-38
[3] prettyunits1.0.2 gtools3.8.1
[5] assertthat0.2.1 digest0.6.23
[7] BiocFileCache1.10.2 R62.4.1
[9] RSQLite2.2.0 httr1.4.1
[11] pillar1.4.2 zlibbioc1.32.0
[13] rlang0.4.5 progress1.2.2
[15] curl4.3 blob1.2.1
[17] Matrix1.2-17 preprocessCore1.48.0
[19] BiocParallel1.20.1 stringr1.4.0
[21] RCurl1.98-1.1 bit1.1-15.2
[23] biomaRt2.42.0 DelayedArray0.12.2
[25] compiler3.6.1 pkgconfig2.0.3
[27] askpass1.1 openssl1.4.1
[29] tidyselect1.0.0 SummarizedExperiment1.16.1 [31] tibble2.1.3 GenomeInfoDbData1.2.2
[33] DNAcopy1.60.0 matrixStats0.55.0
[35] XML3.99-0.3 crayon1.3.4
[37] dplyr0.8.4 dbplyr1.4.2
[39] GenomicAlignments1.22.1 bitops1.0-6
[41] rappdirs0.3.1 grid3.6.1
[43] DBI1.1.0 magrittr1.5
[45] stringi1.4.3 getopt1.20.3
[47] vctrs0.2.3 tools3.6.1
[49] bit640.9-7 Biobase2.46.0
[51] glue1.3.1 purrr0.3.3
[53] hms0.5.3 AnnotationDbi1.48.0
[55] BiocManager1.30.10 memoise1.1.0