Entering edit mode
Hi I have a standard condition KO vs WT and i want to know the exon usage in KO condition. So i used following script
Code should be placed in three backticks as shown below
my_gtf_1 <- makeTxDbFromEnsembl(organism="Homo sapiens",
release=86,
circ_seqs=NULL,
server="ensembldb.ensembl.org",
username="anonymous", password=NULL, port=0L,
tx_attrib=NULL)
nonOverlappingExons <- disjointExons(my_gtf_1)
names(nonOverlappingExons) <- paste(mcols(nonOverlappingExons)$gene_id, mcols(nonOverlappingExons)$exonic_part,sep = "_")
Exon_counts<- summarizeOverlaps(nonOverlappingExons,myBams,ignore.strand = FALSE,inter.feature=FALSE)
ToFilter <- apply(assay(Exon_counts),1,function(x) sum(x > 20)) >= 2
Exon_counts_filtered <- Exon_counts[ToFilter, ]
countMatrix <- assay(Exon_counts_filtered)
countGRanges <- rowRanges(Exon_counts_filtered)
geneIDs <- as.vector(unlist(countGRanges$gene_id))
exonIDs <- rownames(countMatrix)
metaData <- data.frame(condition=c("KO","KO","KO","WT","WT","WT"),row.names=colnames(Exon_counts_filtered))
ddx_1 <- DEXSeqDataSet(countMatrix,metaData,design = ~sample+exon+condition:exon,featureID = exonIDs,groupID = geneIDs)
ddx_1 <- estimateSizeFactors(ddx_1)
ddx_1 <- estimateDispersions(ddx_1)
dxd_1 <- testForDEU(ddx_1)
dxd_1 = estimateExonFoldChanges(dxd_1, fitExpToVar="condition")
dxr = DEXSeqResults(dxd_1)
plotDEXSeq( dxr, "ENSG00000000003", legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 )
**Error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) :
need finite 'ylim' values**
groupID featureID exonBaseMean dispersion stat pvalue padj KO WT log2fold_WT_KO
ENSG00000000003:ENSG00000000003_1 ENSG00000000003 ENSG00000000003_1 237.7838 0.0154993268 3.18606743 0.07426848 0.8995720 21.72677 24.30731 0.37330829
ENSG00000000003:ENSG00000000003_2 ENSG00000000003 ENSG00000000003_2 2697.1990 0.0009817991 0.28744737 0.59186098 0.9596296 55.15708 54.95249 -0.01900645
ENSG00000000003:ENSG00000000003_3 ENSG00000000003 ENSG00000000003_3 756.8533 0.0007919755 0.32614792 0.56793618 0.9571905 36.65145 36.44270 -0.02256554
ENSG00000000003:ENSG00000000003_5 ENSG00000000003 ENSG00000000003_5 568.3346 0.0009387741 0.23865462 0.62517951 0.9625576 32.66184 33.04087 0.04335657
ENSG00000000003:ENSG00000000003_6 ENSG00000000003 ENSG00000000003_6 345.2394 0.0013624177 3.03196976 0.08163885 0.9114054 26.33814 27.56497 0.15860971
ENSG00000000003:ENSG00000000003_7 ENSG00000000003 ENSG00000000003_7 334.3815 0.0025486393 0.02785648 0.86744669 0.9887713 26.45660 26.69058 0.03053553
genomicData countData.SRR1039508_KO_1_Aligned.sortedByCoord.out.bam
ENSG00000000003:ENSG00000000003_1 271
sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.10 DEXSeq_1.38.0
[3] RColorBrewer_1.1-3 DESeq2_1.32.0
[5] BiocParallel_1.26.2 GenomicAlignments_1.28.0
[7] SummarizedExperiment_1.22.0 MatrixGenerics_1.4.3
[9] matrixStats_0.62.0 BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000
[11] BSgenome_1.60.0 rtracklayer_1.52.1
[13] GenomicFeatures_1.44.2 AnnotationDbi_1.54.1
[15] Biobase_2.52.0 Rsamtools_2.8.0
[17] Biostrings_2.60.2 XVector_0.32.0
[19] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4
[21] IRanges_2.26.0 S4Vectors_0.30.2
[23] BiocGenerics_0.38.0 DRIMSeq_1.20.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 lubridate_1.9.0 bit64_4.0.5 filelock_1.0.2
[5] progress_1.2.2 httr_1.4.4 tools_4.1.2 utf8_1.2.2
[9] R6_2.5.1 DBI_1.1.3 colorspace_2.0-3 withr_2.5.0
[13] tidyselect_1.2.0 prettyunits_1.1.1 bit_4.0.5 curl_4.3.3
[17] compiler_4.1.2 cli_3.4.1 xml2_1.3.3 DelayedArray_0.18.0
[21] scales_1.2.1 genefilter_1.74.1 rappdirs_0.3.3 stringr_1.4.1
[25] digest_0.6.30 rmarkdown_2.18 pkgconfig_2.0.3 htmltools_0.5.3
[29] dbplyr_2.2.1 fastmap_1.1.0 limma_3.48.3 RMariaDB_1.2.2
[33] rlang_1.0.6 rstudioapi_0.14 RSQLite_2.2.18 BiocIO_1.2.0
[37] generics_0.1.3 hwriter_1.3.2.1 RCurl_1.98-1.9 magrittr_2.0.3
[41] GenomeInfoDbData_1.2.6 Matrix_1.5-3 Rcpp_1.0.9 munsell_0.5.0
[45] fansi_1.0.3 lifecycle_1.0.3 stringi_1.7.8 yaml_2.3.6
[49] edgeR_3.34.1 zlibbioc_1.38.0 plyr_1.8.8 BiocFileCache_2.0.0
[53] grid_4.1.2 blob_1.2.3 crayon_1.5.2 lattice_0.20-45
[57] splines_4.1.2 annotate_1.70.0 hms_1.1.2 KEGGREST_1.32.0
[61] locfit_1.5-9.6 knitr_1.40 pillar_1.8.1 rjson_0.2.21
[65] geneplotter_1.70.0 reshape2_1.4.4 biomaRt_2.48.3 XML_3.99-0.12
[69] glue_1.6.2 evaluate_0.18 png_0.1-7 vctrs_0.5.1
[73] gtable_0.3.1 assertthat_0.2.1 cachem_1.0.6 ggplot2_3.4.0
[77] xfun_0.35 xtable_1.8-4 restfulr_0.0.15 survival_3.4-0
[81] tibble_3.1.8 memoise_2.0.1 timechange_0.1.1 statmod_1.4.37
[85] ellipsis_0.3.2
My DEXSeq final table looks fine
table( dxr$padj < 0.05 )
FALSE TRUE
323011 777
But still i'm getting this error which i have no clue?
Could you share
dput(dxr[dxr$groupID=="ENSG00000000003",])
to make your issue reproducible please ? Thanks