Closed Pentayouth closed 2 years ago
charles-plessy
commented
2 years ago Thanks for the report, can you share small-size bam files that reproduce the error? If subsetting in a small region is not enough, try subsetting two regions from two different chromosomes, making sure that there is signal on both strands. Hopefully that would be enough.
Pentayouth
commented
2 years ago Thank you for your kind reply. I'm happy to share my bam file but I don't know how. Can you download from the link below? The file size is ~8M. https://pan.baidu.com/s/1BqclqGIZGZ-2gXykgSUAFA The share password is 451f
Pentayouth
commented
2 years ago BTW, the code that generated the small bam is:
samtools view -Sb rrna_rm.markdup.bam chr21 chr22 > *.small.bam
Pentayouth
commented
2 years ago I really appreciate the chance to have a direct contact with you the developer. So I would like to ask 2 more questions and hope for your clarification.
correctSystematicG = TRUE, but I got an error which said correctSystematicG = TRUE currently doesnt support CAGEexp object. It looks wired to me, could you please explain it?
Thank you in advance for any reply or suggestion.
Wangcharles-plessy
commented
2 years ago Can you download from the link below?
Sorry, but I have an error message that Google Translate says it means the link is expired. Since the file is only 8M, can you e-mail it to me? My maintainer address is charles.plessy at oist.jp.
Pentayouth
commented
2 years ago Sure, I've send it to you. Please let me know if everything works fine.
charles-plessy
commented
2 years ago 1. After I failed to input bam, I tried to input data in another way like inputing ctss file. But from the vignette I can't find any clue about how to generate such file. I understand the definition of CTSS, but I wonder if *.ctss format is formaly defined.
CTSS is a format that was used in an earlier FANTOM project; I would not recommend it today. Can you try converting to BED and using the bed format ?
2. When getCTSS(), I can't specify `correctSystematicG = TRUE`, but I got an error which said `correctSystematicG = TRUE` currently doesnt support CAGEexp object. It looks wired to me, could you please explain it?
In BAM files where 5-prime mismatches are not soft-clipped (which was the standard when CAGEr was created), the alignment can start on a mismatched G that was added by the reverse-transcriptase, and the removeFirstG option corrects that. Very often, it is enough. But what if a G was added and matches by chance a G in the genome ? The correctSystematicG is an attempt to solve that question. It is a more complex algorithm and when I replaced the CAGEset class by the more efficient CAGEexp class, I did not find time to port it.
charles-plessy
commented
2 years ago On my computer it works, but I only have time to test on a container with R-dev and Bioc devel version. Can you double-check that the files you sent me trigger the error on your side ?
> inputFiles <- c("cjc.small.bam", "xxz.small.bam")
>
> ce_nepc <- CAGEexp(genomeName = "BSgenome.Hsapiens.UCSC.hg38",
+ inputFiles = inputFiles,
+ inputFilesType = "bamPairedEnd",
+ sampleLabels = c("cjc","xxz"))
> ce_nepc
A CAGEexp object of 0 listed
experiments with no user-defined names and respective classes.
Containing an ExperimentList class object of length 0:
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
>
> ce_nepc <- getCTSS(ce_nepc, correctSystematicG = FALSE)
Reading in file: cjc.small.bam...
-> Filtering out low quality reads...
-> Removing the first base of the reads if 'G' and not aligned to the genome...
Reading in file: xxz.small.bam...
-> Filtering out low quality reads...
-> Removing the first base of the reads if 'G' and not aligned to the genome...
>
> colData(ce_nepc)
DataFrame with 2 rows and 4 columns
inputFiles inputFilesType sampleLabels librarySizes
<character> <character> <character> <integer>
cjc cjc.small.bam bamPairedEnd cjc 18887
xxz xxz.small.bam bamPairedEnd xxz 92637
>
> CTSScoordinatesGR(ce_nepc)
CTSS object with 11141 positions and 0 metadata columns:
seqnames pos strand
<Rle> <integer> <Rle>
[1] chr21 5096795 +
[2] chr21 5101807 +
[3] chr21 5118090 +
[4] chr21 5123229 +
[5] chr21 6564651 +
... ... ... ...
[11137] chr22 50783636 -
[11138] chr22 50783641 -
[11139] chr22 50783642 -
[11140] chr22 50783646 -
[11141] chr22 50783652 -
-------
seqinfo: 640 sequences (1 circular) from hg38 genome
BSgenome name: BSgenome.Hsapiens.UCSC.hg38
>
> sessionInfo()
R Under development (unstable) (2021-10-27 r81107)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] CAGEr_2.1.0 MultiAssayExperiment_1.21.0 SummarizedExperiment_1.25.0 Biobase_2.55.0 GenomicRanges_1.46.0 GenomeInfoDb_1.31.0
[7] IRanges_2.29.0 S4Vectors_0.33.0 BiocGenerics_0.41.0 MatrixGenerics_1.7.0 matrixStats_0.61.0
loaded via a namespace (and not attached):
[1] VGAM_1.1-5 splines_4.2.0 DelayedMatrixStats_1.17.0 gtools_3.9.2 assertthat_0.2.1
[6] BiocManager_1.30.16 BSgenome_1.63.0 GenomeInfoDbData_1.2.7 Rsamtools_2.11.0 yaml_2.2.1
[11] pillar_1.6.4 lattice_0.20-45 glue_1.4.2 XVector_0.35.0 colorspace_2.0-2
[16] Matrix_1.3-4 plyr_1.8.6 XML_3.99-0.8 pkgconfig_2.0.3 zlibbioc_1.41.0
[21] purrr_0.3.4 scales_1.1.1 stringdist_0.9.8 BiocParallel_1.29.0 tibble_3.1.5
[26] mgcv_1.8-38 generics_0.1.1 ggplot2_3.3.5 ellipsis_0.3.2 cachem_1.0.6
[31] formula.tools_1.7.1 magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0 fansi_0.5.0
[36] nlme_3.1-153 operator.tools_1.6.3 MASS_7.3-54 vegan_2.5-7 tools_4.2.0
[41] data.table_1.14.2 BiocIO_1.5.0 lifecycle_1.0.1 stringr_1.4.0 munsell_0.5.0
[46] cluster_2.1.2 DelayedArray_0.21.0 Biostrings_2.63.0 som_0.3-5.1 compiler_4.2.0
[51] rlang_0.4.12 grid_4.2.0 RCurl_1.98-1.5 rstudioapi_0.13 rjson_0.2.20
[56] bitops_1.0-7 restfulr_0.0.13 gtable_0.3.0 DBI_1.1.1 reshape2_1.4.4
[61] R6_2.5.1 GenomicAlignments_1.31.0 dplyr_1.0.7 rtracklayer_1.55.0 fastmap_1.1.0
[66] utf8_1.2.2 KernSmooth_2.23-20 permute_0.9-5 stringi_1.7.5 parallel_4.2.0
[71] Rcpp_1.0.7 vctrs_0.3.8 BSgenome.Hsapiens.UCSC.hg38_1.4.4 tidyselect_1.1.1 sparseMatrixStats_1.7.0 Maybe there is an issue with my conda environment or somthing... I feel sorry to have bothered you,
Anyway, thank you so much for your time. You are so nice. Have a nice day ;-)
charles-plessy
commented
2 years ago No worries !
I am going to close this issue, but feel free to reopen it if you can reproduce it on a fresh package.
Pentayouth
commented
2 years ago Hello Plessy, I don't want to bother you but as I switched from the lab Linux server to my personal windows PC, the same error still exists... Here's the code and the sessioninfo.
This time I used CAGEr 2.1.0 instead of 2.0.1, so I installed the github version by devtools::install_local()
rm(list = ls())
# install.packages("pacman")
# install.packages("installr")
library(pacman)
# require(installr)
# updateR()
p_unload(CAGEr)
devtools::install_local("./CAGEr-master.zip") # try to install github version
library(CAGEr)
library(rtracklayer)
library(dplyr)
# BiocManager::install("CAGEr", force = T)
# chooseBioCmirror()
# BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
inputFiles = paste0(getwd(),"/",c("CJC","XXZ"),"/rrna_rm.markdup.bam"); file.exists(inputFiles)
ce_nepc <- CAGEexp(genomeName = "BSgenome.Hsapiens.UCSC.hg38",
inputFiles = inputFiles,
inputFilesType = "bamPairedEnd",
sampleLabels = c("cjc","xxz")); ce_nepc
getCTSS(ce_nepc, correctSystematicG = F)
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] CAGEr_2.1.1 pacman_0.5.1 MultiAssayExperiment_1.20.0
[4] SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.0
[7] GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.2
[10] BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.61.0
loaded via a namespace (and not attached):
[1] nlme_3.1-153 bitops_1.0-7 fs_1.5.0 usethis_2.1.3
[5] devtools_2.4.2 rprojroot_2.0.2 tools_4.1.2 utf8_1.2.2
[9] R6_2.5.1 vegan_2.5-7 KernSmooth_2.23-20 mgcv_1.8-38
[13] colorspace_2.0-2 permute_0.9-5 withr_2.4.2 tidyselect_1.1.1
[17] prettyunits_1.1.1 processx_3.5.2 compiler_4.1.2 cli_3.1.0
[21] desc_1.4.0 DelayedArray_0.20.0 rtracklayer_1.54.0 scales_1.1.1
[25] callr_3.7.0 stringr_1.4.0 Rsamtools_2.10.0 stringdist_0.9.8
[29] XVector_0.34.0 pkgconfig_2.0.3 sessioninfo_1.2.1 sparseMatrixStats_1.6.0
[33] fastmap_1.1.0 BSgenome_1.62.0 rlang_0.4.12 rstudioapi_0.13
[37] VGAM_1.1-5 DelayedMatrixStats_1.16.0 BiocIO_1.4.0 generics_0.1.1
[41] BiocParallel_1.28.0 gtools_3.9.2 dplyr_1.0.7 RCurl_1.98-1.5
[45] magrittr_2.0.1 GenomeInfoDbData_1.2.7 Matrix_1.3-4 Rcpp_1.0.7
[49] munsell_0.5.0 fansi_0.5.0 lifecycle_1.0.1 stringi_1.7.5
[53] yaml_2.2.1 MASS_7.3-54 zlibbioc_1.40.0 pkgbuild_1.2.0
[57] plyr_1.8.6 grid_4.1.2 formula.tools_1.7.1 parallel_4.1.2
[61] crayon_1.4.2 lattice_0.20-45 Biostrings_2.62.0 splines_4.1.2
[65] ps_1.6.0 pillar_1.6.4 rjson_0.2.20 reshape2_1.4.4
[69] pkgload_1.2.3 XML_3.99-0.8 glue_1.4.2 data.table_1.14.2
[73] remotes_2.4.1 operator.tools_1.6.3 vctrs_0.3.8 testthat_3.1.0
[77] gtable_0.3.0 purrr_0.3.4 cachem_1.0.6 ggplot2_3.3.5
[81] restfulr_0.0.13 tibble_3.1.5 som_0.3-5.1 GenomicAlignments_1.30.0
[85] memoise_2.0.0 cluster_2.1.2 ellipsis_0.3.2 I've sent you the bam files I used that contain reads from all chromosomes by e-mail in case you are interested.
Best regards. Wang
charles-plessy
commented
2 years ago Thanks for your investigation! I could reproduce the bug with 2.0.1 in a different container.
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] CAGEr_2.0.1 MultiAssayExperiment_1.20.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
[7] IRanges_2.28.0 S4Vectors_0.32.2 BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.61.0
loaded via a namespace (and not attached):
[1] VGAM_1.1-5 splines_4.1.1 DelayedMatrixStats_1.16.0 gtools_3.9.2 assertthat_0.2.1
[6] BiocManager_1.30.16 BSgenome_1.62.0 GenomeInfoDbData_1.2.7 Rsamtools_2.10.0 yaml_2.2.1
[11] pillar_1.6.4 lattice_0.20-45 glue_1.5.0 XVector_0.34.0 colorspace_2.0-2
[16] Matrix_1.3-4 plyr_1.8.6 XML_3.99-0.8 pkgconfig_2.0.3 zlibbioc_1.40.0
[21] purrr_0.3.4 scales_1.1.1 stringdist_0.9.8 BiocParallel_1.28.0 tibble_3.1.6
[26] mgcv_1.8-38 generics_0.1.1 ggplot2_3.3.5 ellipsis_0.3.2 cachem_1.0.6
[31] formula.tools_1.7.1 magrittr_2.0.1 crayon_1.4.2 memoise_2.0.0 fansi_0.5.0
[36] operator.tools_1.6.3 nlme_3.1-153 MASS_7.3-54 vegan_2.5-7 tools_4.1.1
[41] data.table_1.14.2 BiocIO_1.4.0 lifecycle_1.0.1 stringr_1.4.0 munsell_0.5.0
[46] cluster_2.1.2 DelayedArray_0.20.0 Biostrings_2.62.0 som_0.3-5.1 compiler_4.1.1
[51] rlang_0.4.12 grid_4.1.1 RCurl_1.98-1.5 rstudioapi_0.13 rjson_0.2.20
[56] bitops_1.0-7 restfulr_0.0.13 gtable_0.3.0 DBI_1.1.1 reshape2_1.4.4
[61] R6_2.5.1 GenomicAlignments_1.30.0 dplyr_1.0.7 rtracklayer_1.54.0 fastmap_1.1.0
[66] utf8_1.2.2 KernSmooth_2.23-20 permute_0.9-5 stringi_1.7.5 parallel_4.1.1
[71] Rcpp_1.0.7 vctrs_0.3.8 BSgenome.Hsapiens.UCSC.hg38_1.4.4 tidyselect_1.1.1 sparseMatrixStats_1.6.0I think that I isolated the problem. I do not understand why the error did not trigger earlier on my machine. Basically, the promoters function fails on GPos objects, and the CTSS class is wrapping the GPos class...
> promoters(CTSScoordinatesGR(exampleCAGEexp))
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘update_ranges’ for signature ‘"UnstitchedIPos"’
> promoters(GRanges(CTSScoordinatesGR(exampleCAGEexp)))
GRanges object with 5000 ranges and 5 metadata columns:
seqnames ranges strand | genes annotation exprClass filteredCTSSidx cluster
<Rle> <IRanges> <Rle> | <Rle> <Rle> <Rle> <Rle> <Rle>
[1] chr17 26025430-26027629 + | unknown 0_0 TRUE chr17:26027430:+
[2] chr17 26048540-26050739 + | grid1a promoter 4_4 TRUE chr17:26050540:+
[3] chr17 26116088-26118287 + | grid1a exon 0_0 TRUE chr17:26118088:+
[4] chr17 26140853-26143052 + | grid1a intron 0_4 TRUE chr17:26142853:+
[5] chr17 26164954-26167153 + | grid1a exon 0_0 TRUE chr17:26166954:+
... ... ... ... . ... ... ... ... ...
[4996] chr17 32706950-32709149 + | ywhaqb exon 0_2 TRUE chr17:32708847-32708..
[4997] chr17 32706953-32709152 + | ywhaqb exon 0_2 TRUE chr17:32708847-32708..
[4998] chr17 32706955-32709154 + | ywhaqb exon 0_2 TRUE chr17:32708847-32708..
[4999] chr17 32706957-32709156 + | ywhaqb exon 0_4 TRUE chr17:32708847-32708..
[5000] chr17 32706958-32709157 + | ywhaqb exon 0_2 TRUE chr17:32708847-32708..
-------
seqinfo: 26 sequences (1 circular) from danRer7 genomeFor the record, I am asking upstream if this failure is expected: https://support.bioconductor.org/p/9140695/
Pentayouth
commented
2 years ago Hello, Plessy
Thank you for your reply. I'm very glad that I helped.
There are promotors() function in
SummarizedExperiment
GenomicFeatures
GenomicRanges
IRanges
So I wonder which one you actually specified here. Also why does the error only occurs in certain circumstance.
Best Regards, Wang
charles-plessy
commented
2 years ago I think that I fixed the issue in the master branch. Can you install it and check you can load your data? If yes I will port the fix to the stable version, which will be 2.0.2.
Pentayouth
commented
2 years ago Hello Plessy,
Sorry for the late reply.
I have tested the latest branch, everything works fine!
Thank you for all your kindness and patience.
Best
Wang
> devtools::install_local("./CAGEr-master.zip")
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: glue (1.4.2 -> 1.5.0) [CRAN]
5: tibble (3.1.5 -> 3.1.6) [CRAN]
Enter one or more numbers, or an empty line to skip updates: library(CAGEr)
Enter one or more numbers, or an empty line to skip updates: 3
* installing *source* package 'CAGEr' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CAGEr'
finding HTML links ... done
CAGEexp-class html
finding level-2 HTML links ... done
CAGEr-class html
CAGEr-package html
CAGEr_Multicore html
CTSS-class html
CTSSclusteringMethod html
CTSScoordinates html
CTSScumulativesTagClusters html
CTSSnormalizedTpm html
CTSStagCount html
CTSStoGenes html
ConsensusClusters-class html
CustomConsensusClusters html
FANTOM5humanSamples html
FANTOM5mouseSamples html
GeneExpDESeq2 html
GeneExpSE html
QuantileWidthFunctions html
TagClusters-class html
aggregateTagClusters html
annotateCTSS html
bam2CTSS html
byCtss html
clusterAggregateAndSum html
clusterCTSS html
coerceInBSgenome html
consensusClusterConvertors html
consensusClusters-set html
consensusClusters html
consensusClustersDESeq2 html
consensusClustersQuantile html
consensusClustersTpm html
coverage-functions html
cumulativeCTSSdistribution html
distclu-functions html
exampleCAGEexp html
exampleZv9_annot html
exportToTrack html
expressionClasses html
genomeName html
getCTSS html
getExpressionProfiles html
getShiftingPromoters html
hanabi-class html
hanabi html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Program Files/R/R-4.1.2/library/00LOCK-CAGEr-master/00new/CAGEr/help/hanabi+2Clist-method.html
hanabiPlot html
import.CAGEscanMolecule html
import.CTSS html
import.bam html
import.bam.ctss html
import.bedCTSS html
import.bedScore html
import.bedmolecule html
inputFiles html
inputFilesType html
librarySizes html
loadFileIntoGPos html
mapStats html
mapStatsScopes html
mergeCAGEsets html
mergeSamples html
moleculesGR2CTSS html
normalizeTagCount html
parseCAGEscanBlocksToGrangeTSS html
plot.hanabi html
plotAnnot html
plotCorrelation html
plotExpressionProfiles html
plotInterquantileWidth html
plotReverseCumulatives html
powerLaw html
quantilePositions html
ranges2annot html
ranges2genes html
ranges2names html
sampleLabels html
scoreShift html
seqNameTotalsSE html
setColors html
strandInvaders html
summariseChrExpr html
tagClusters html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (CAGEr)
> library(CAGEr)
载入需要的程辑包：MultiAssayExperiment
载入需要的程辑包：SummarizedExperiment
载入需要的程辑包：MatrixGenerics
载入需要的程辑包：matrixStats
载入程辑包：‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins,
colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads,
colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges,
colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs,
rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs,
rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads,
rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars
载入需要的程辑包：GenomicRanges
载入需要的程辑包：stats4
载入需要的程辑包：BiocGenerics
载入程辑包：‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated,
eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min
载入需要的程辑包：S4Vectors
载入程辑包：‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
载入需要的程辑包：IRanges
载入程辑包：‘IRanges’
The following object is masked from ‘package:grDevices’:
windows
载入需要的程辑包：GenomeInfoDb
载入需要的程辑包：Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
see 'citation("Biobase")', and for packages 'citation("pkgname")'.
载入程辑包：‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
> getwd()
[1] "C:/Users/PtaYoth/Desktop/cage"
> inputFiles = paste0(getwd(),"/",c("CJC","XXZ"),"/rrna_rm.markdup.bam"); file.exists(inputFiles)
[1] TRUE TRUE
> ce_nepc <- CAGEexp(genomeName = "BSgenome.Hsapiens.UCSC.hg38",
+ inputFiles = inputFiles,
+ inputFilesType = "bamPairedEnd",
+ sampleLabels = c("cjc","xxz")); ce_nepc
A CAGEexp object of 0 listed
experiments with no user-defined names and respective classes.
Containing an ExperimentList class object of length 0:
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
> getCTSS(ce_nepc, correctSystematicG = F)
Reading in file: C:/Users/PtaYoth/Desktop/cage/CJC/rrna_rm.markdup.bam...
-> Filtering out low quality reads...
载入需要的名字空间：BSgenome.Hsapiens.UCSC.hg38
-> Removing the first base of the reads if 'G' and not aligned to the genome...
Reading in file: C:/Users/PtaYoth/Desktop/cage/XXZ/rrna_rm.markdup.bam...
-> Filtering out low quality reads...
-> Removing the first base of the reads if 'G' and not aligned to the genome...
A CAGEexp object of 1 listed
experiment with a user-defined name and respective class.
Containing an ExperimentList class object of length 1:
[1] tagCountMatrix: RangedSummarizedExperiment with 348135 rows and 2 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] CAGEr_2.1.1 MultiAssayExperiment_1.20.0 SummarizedExperiment_1.24.0
[4] Biobase_2.54.0 GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
[7] IRanges_2.28.0 S4Vectors_0.32.2 BiocGenerics_0.40.0
[10] MatrixGenerics_1.6.0 matrixStats_0.61.0
loaded via a namespace (and not attached):
[1] nlme_3.1-153 bitops_1.0-7 fs_1.5.0
[4] usethis_2.1.3 devtools_2.4.2 rprojroot_2.0.2
[7] tools_4.1.2 utf8_1.2.2 R6_2.5.1
[10] vegan_2.5-7 KernSmooth_2.23-20 mgcv_1.8-38
[13] DBI_1.1.1 colorspace_2.0-2 permute_0.9-5
[16] withr_2.4.2 tidyselect_1.1.1 prettyunits_1.1.1
[19] processx_3.5.2 compiler_4.1.2 cli_3.1.0
[22] desc_1.4.0 DelayedArray_0.20.0 rtracklayer_1.54.0
[25] scales_1.1.1 callr_3.7.0 stringr_1.4.0
[28] Rsamtools_2.10.0 stringdist_0.9.8 XVector_0.34.0
[31] pkgconfig_2.0.3 sessioninfo_1.2.1 sparseMatrixStats_1.6.0
[34] fastmap_1.1.0 BSgenome_1.62.0 rlang_0.4.12
[37] rstudioapi_0.13 VGAM_1.1-5 DelayedMatrixStats_1.16.0
[40] BiocIO_1.4.0 generics_0.1.1 BiocParallel_1.28.0
[43] gtools_3.9.2 dplyr_1.0.7 RCurl_1.98-1.5
[46] magrittr_2.0.1 GenomeInfoDbData_1.2.7 Matrix_1.3-4
[49] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
[52] lifecycle_1.0.1 stringi_1.7.5 yaml_2.2.1
[55] MASS_7.3-54 zlibbioc_1.40.0 pkgbuild_1.2.0
[58] plyr_1.8.6 grid_4.1.2 formula.tools_1.7.1
[61] parallel_4.1.2 crayon_1.4.2 lattice_0.20-45
[64] Biostrings_2.62.0 splines_4.1.2 BSgenome.Hsapiens.UCSC.hg38_1.4.4
[67] ps_1.6.0 pillar_1.6.4 rjson_0.2.20
[70] reshape2_1.4.4 pkgload_1.2.3 XML_3.99-0.8
[73] glue_1.4.2 data.table_1.14.2 remotes_2.4.1
[76] operator.tools_1.6.3 vctrs_0.3.8 testthat_3.1.0
[79] gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1
[82] cachem_1.0.6 ggplot2_3.3.5 restfulr_0.0.13
[85] tibble_3.1.5 som_0.3-5.1 GenomicAlignments_1.30.0
[88] memoise_2.0.0 cluster_2.1.2 ellipsis_0.3.2 Thank you too; the size-reduced BAM files that you sent me were instrumental in solving that bug.
I wanted to getCTSS directly from PE bam file. I did:
It works well with CAGEr 1.34.0, but I want to use
exportToTrack(), so I updated to CAGEr 2.0.1, however, the same code gives an Error this time:I googled for solution and just found one relevant post here: https://stat.ethz.ch/pipermail/bioc-devel/2019-September/015524.html which saied:
I have no idea, but something must be wrong.
My session info is: