Entering edit mode
Hello,
I am trying to do a ChIPQC analysis, but it appears that annotations for Saccharomyces Cerevisiae are not supported:
> library(ChIPQC)
> samples = read.csv("sample.sheet.csv")
> CQCanalysis = ChIPQC(samples, annotation="sacCer3")
swn1 WT none 1 macs
swn2 WT none 2 macs
swh1 WT hs 1 macs
swh2 WT hs 2 macs
smn1 MT none 1 macs
smn2 MT none 2 macs
smh1 MT hs 1 macs
smh2 MT hs 2 macs
Checking chromosomes:
[1] "chrI"
Compiling annotation...
Error in getAnnotation(annotation, AllChr = chromosomes) :
Unsupported annotation:sacCer3
After reading a bit further, I understand you can create a custom gene annotation, so I tried the following:
> library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
> library(GenomicRanges)
> library(ChIPpeakAnno)
> yGR <- toGRanges(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
> yGR
GRanges object with 6534 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
Q0010 chrM 3952-4415 +
Q0032 chrM 11667-11957 +
Q0055 chrM 13818-26701 +
Q0075 chrM 24156-25255 +
Q0080 chrM 27666-27812 +
... ... ... ...
YPR200C chrXVI 939279-939671 -
YPR201W chrXVI 939922-941136 +
YPR202W chrXVI 943032-944188 +
YPR204C-A chrXVI 946856-947338 -
YPR204W chrXVI 944603-947701 +
-------
seqinfo: 17 sequences (1 circular) from sacCer3 genome
> customAnno <- list(version="sacCer3", Test=yGR)
> CQCanalysis = ChIPQC(samples, annotation="customAnno")
swn1 WT none 1 macs
swn2 WT none 2 macs
swh1 WT hs 1 macs
swh2 WT hs 2 macs
smn1 MT none 1 macs
smn2 MT none 2 macs
smh1 MT hs 1 macs
smh2 MT hs 2 macs
Checking chromosomes:
[1] "chrI"
Compiling annotation...
Error in getAnnotation(annotation, AllChr = chromosomes) :
Unsupported annotation:customAnno
Any advice would be appreciated,
Thanks,
Ben
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] ChIPpeakAnno_3.18.0 VennDiagram_1.6.20
[3] futile.logger_1.4.3 Biostrings_2.52.0
[5] XVector_0.24.0 TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2
[7] GenomicFeatures_1.36.0 AnnotationDbi_1.46.0
[9] ChIPQC_1.20.0 DiffBind_2.12.0
[11] SummarizedExperiment_1.14.0 DelayedArray_0.10.0
[13] BiocParallel_1.17.18 matrixStats_0.54.0
[15] Biobase_2.44.0 GenomicRanges_1.36.0
[17] GenomeInfoDb_1.20.0 IRanges_2.18.0
[19] S4Vectors_0.22.0 BiocGenerics_0.30.0
[21] ggplot2_3.1.1
loaded via a namespace (and not attached):
[1] amap_0.8-16 colorspace_1.4-1
[3] seqinr_3.4-5 rjson_0.2.20
[5] hwriter_1.3.2 ggrepel_0.8.1
[7] bit64_0.9-7 splines_3.6.0
[9] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 ade4_1.7-13
[11] Nozzle.R1_1.1-1 Rsamtools_2.0.0
[13] annotate_1.62.0 GO.db_3.8.2
[15] pheatmap_1.0.12 graph_1.62.0
[17] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2 BiocManager_1.30.4
[19] compiler_3.6.0 httr_1.4.0
[21] GOstats_2.50.0 backports_1.1.4
[23] assertthat_0.2.1 Matrix_1.2-17
[25] lazyeval_0.2.2 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[27] limma_3.40.0 formatR_1.6
[29] prettyunits_1.0.2 tools_3.6.0
[31] gtable_0.3.0 glue_1.3.1
[33] GenomeInfoDbData_1.2.1 Category_2.50.0
[35] reshape2_1.4.3 systemPipeR_1.18.0
[37] dplyr_0.8.0.1 batchtools_0.9.11
[39] rappdirs_0.3.1 ShortRead_1.42.0
[41] Rcpp_1.0.1 TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[43] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 multtest_2.40.0
[45] gdata_2.18.0 rtracklayer_1.44.0
[47] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7 stringr_1.4.0
[49] ensembldb_2.8.0 gtools_3.8.1
[51] XML_3.98-1.19 idr_1.2
[53] edgeR_3.26.1 MASS_7.3-51.4
[55] zlibbioc_1.30.0 scales_1.0.0
[57] BSgenome_1.52.0 VariantAnnotation_1.30.0
[59] ProtGenerics_1.16.0 hms_0.4.2
[61] RBGL_1.60.0 AnnotationFilter_1.8.0
[63] lambda.r_1.2.3 RColorBrewer_1.1-2
[65] curl_3.3 yaml_2.2.0
[67] memoise_1.1.0 biomaRt_2.40.0
[69] latticeExtra_0.6-28 stringi_1.4.3
[71] RSQLite_2.1.1 genefilter_1.66.0
[73] checkmate_1.9.3 caTools_1.17.1.2
[75] chipseq_1.34.0 rlang_0.3.4
[77] pkgconfig_2.0.2 bitops_1.0-6
[79] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2 lattice_0.20-38
[81] purrr_0.3.2 GenomicAlignments_1.20.0
[83] bit_1.1-14 tidyselect_0.2.5
[85] GSEABase_1.46.0 AnnotationForge_1.26.0
[87] plyr_1.8.4 magrittr_1.5
[89] R6_2.4.0 gplots_3.0.1.1
[91] base64url_1.4 DBI_1.0.0
[93] pillar_1.4.0 withr_2.1.2
[95] survival_2.44-1.1 RCurl_1.95-4.12
[97] tibble_2.1.1 crayon_1.3.4
[99] futile.options_1.0.1 KernSmooth_2.23-15
[101] progress_1.2.1 locfit_1.5-9.1
[103] data.table_1.12.2 blob_1.1.1
[105] Rgraphviz_2.28.0 digest_0.6.18
[107] xtable_1.8-4 regioneR_1.16.1
[109] brew_1.0-6 munsell_0.5.0
CQCanalysis = ChIPQC(samples, annotation="customAnno")I think you could remove quotation marks, and following command will works.
CQCanalysis = ChIPQC(samples, annotation=customAnno)