Dear @lgeistlinger,
moving from email where I tried to reach you for a specific error appeared when trying to implement CNVRanger for 34 WES samples from colorectal cancer patients:
briefly, based on an international collaborative project between DKFZ and other Greek research institutions regarding personalized medicine in cancer (http://www.accc.gr/aboutACCC_info.html), we have acquired around 34 samples with DNA and RNA which were sequenced and pre-processed in the DKFZ bioinformatics facility. Overall, my major goal is to investigate, if there any specific mutational patterns in any of the 3 separated groups of patients, that might interrelate the presence of specific mutational patterns (KRASonly, BRAFonly and wild type), as the ultimate goal is to investigate the molecular landscape of these 3 defined groups-we also utilize additionally public TCGA data to enhance our sample size-
My major question would be for the actual analysis of the CNV data from our 34 patients-as already copy number alterations were called with cnvkit, and as a further step purity and ploidy estimated; for a start, I tried to analyze all data collectively, based on the segmented log2 rations, as in your vignette, with the following code:
head(DT)
# A tibble: 6 x 5
file chromosome start end log2
<chr> <chr> <int> <int> <dbl>
1 CRC_ACCC_01 1 12080 3743427 0.191
2 CRC_ACCC_01 1 3745760 12942340 0.00996
3 CRC_ACCC_01 1 12942900 13802754 -0.278
4 CRC_ACCC_01 1 13803254 43766223 -0.0250
5 CRC_ACCC_01 1 43766723 44684459 0.107
6 CRC_ACCC_01 1 44684588 103345463 -0.0443
smean <- DT$log2
state <- round(2^smean * 2)
state[state > 4] <- 4
DT$log2 <- state
names(DT)[names(DT) == "log2"] <- "state"
DT <- DT[DT$state != 2,]
head(DT)
# A tibble: 6 x 5
file chromosome start end state
<chr> <chr> <int> <int> <dbl>
1 CRC_ACCC_01 1 109778935 109823258 3
2 CRC_ACCC_01 1 152080055 152329130 3
3 CRC_ACCC_01 2 10500 28856096 3
4 CRC_ACCC_01 2 28863705 71742899 3
5 CRC_ACCC_01 2 71743258 74786985 3
6 CRC_ACCC_01 2 74787273 92325671 3
grl <- GenomicRanges::makeGRangesListFromDataFrame(DT, split.field="file", keep.extra.columns=TRUE)
saveRDS(grl, file = "Input.test.grl.CRC.rds")
grl.2 <- populationRanges(grl, density=0.1, est.recur=FALSE)
sel.freq.grl <- subset(grl.2, freq > 1)
library(EnsDb.Hsapiens.v75)
human.hg19.genes <- ensembldb::genes(EnsDb.Hsapiens.v75)
sel.hg19.genes <- subset(human.hg19.genes, gene_biotype == "protein_coding")
olaps <- GenomicRanges::findOverlaps(sel.hg19.genes, sel.freq.grl, ignore.strand=TRUE)
qh <- S4Vectors::queryHits(olaps)
sh <- S4Vectors::subjectHits(olaps)
cgenes <- sel.hg19.genes[qh]
cgenes$type <- sel.freq.grl$type[sh]
However, initially in the following step of trying the visualization through the function cnvOncoPrint:
cnvOncoPrint(sel.freq.grl, cgenes, top.features=15, top.samples = 34)
Error in as(calls, "RaggedExperiment") :
no method or default for coercing "GRanges" to "RaggedExperiment"
cnvOncoPrint(grl, cgenes, top.features=15, top.samples = 34)
Following `at` are removed: GAIN1, GAIN2, because no color was defined for them.
Error: Length of `graphics` should be the same as number of labels.
Thus, in your opinion, how this error could be fixed? It is something wrong with any of the input files? For simplicity I have attached also the initial created GRangeslist object;
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
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] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] EnsDb.Hsapiens.v75_2.99.0 ensembldb_2.17.4 AnnotationFilter_1.17.1
[4] GenomicFeatures_1.45.2 AnnotationDbi_1.55.1 Biobase_2.53.0
[7] CNVRanger_1.9.0 RaggedExperiment_1.17.4 GenomicRanges_1.45.0
[10] GenomeInfoDb_1.29.8 IRanges_2.27.2 S4Vectors_0.31.5
[13] BiocGenerics_0.39.2 data.table_1.14.2 forcats_0.5.1
[16] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[19] readr_2.0.2 tidyr_1.1.4 tibble_3.1.5
[22] ggplot2_3.3.5 tidyverse_1.3.1
Input.test.grl.CRC.rds.zip
With Kind Regards,
Efstathios
Dear @lgeistlinger,
moving from email where I tried to reach you for a specific error appeared when trying to implement CNVRanger for 34 WES samples from colorectal cancer patients:
briefly, based on an international collaborative project between DKFZ and other Greek research institutions regarding personalized medicine in cancer (http://www.accc.gr/aboutACCC_info.html), we have acquired around 34 samples with DNA and RNA which were sequenced and pre-processed in the DKFZ bioinformatics facility. Overall, my major goal is to investigate, if there any specific mutational patterns in any of the 3 separated groups of patients, that might interrelate the presence of specific mutational patterns (KRASonly, BRAFonly and wild type), as the ultimate goal is to investigate the molecular landscape of these 3 defined groups-we also utilize additionally public TCGA data to enhance our sample size-
My major question would be for the actual analysis of the CNV data from our 34 patients-as already copy number alterations were called with cnvkit, and as a further step purity and ploidy estimated; for a start, I tried to analyze all data collectively, based on the segmented log2 rations, as in your vignette, with the following code:
Thus, in your opinion, how this error could be fixed? It is something wrong with any of the input files? For simplicity I have attached also the initial created GRangeslist object;
Input.test.grl.CRC.rds.zip
With Kind Regards,
Efstathios