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Could now apply CAMDAC into WGBS bam file?
Hi, dear guys, @NMNS93 @elarosecadieux ,
I have read your CAMDAC user manual, and I think it a very powerful tool for DNA methylation analysis. So I am extremely excited and want to hand my data using CAMDAC as soon as possible. However, my data are WGBS's bam file. So you mentioned "This flag will become relevant in future CAMDAC versions compatible with WGBS data." in the CAMDAC user manual, I wonder that now could we apply CAMDAC into WGBS bam data? If okay, how should I do to let it work well?
Error when calling ascat.runAscat from run_ASCAT.m
Hi @elarosecadieux ,
First of all, many thanks and congratulations for your work.
I've been exploring CAMDAC as an alternative to the ASCAT cellularity estimates included in the Metabric data (although I'm not sure how different these would be), but I am encountering some issues.
Firstly, I was getting some error when the MspI fragments plots was intended to be saved, but I circumvented it by commenting out the plotting code.
Most importantly, though, I receive the following error message after the "ASCAT copy number segmentation" step has been completed:
Error in `[.data.table`(SNPpos, names(bafsegmented), ) :
When i is a data.table (or character vector), the columns to join by must be specified using 'on=' argument (see ?data.table), by keying x (i.e. sorted, and, marked as sorted, see ?setkey), or by sharing column names between x and i (i.e., a natural join). Keyed joins might have further speed benefits on very large data due to x being sorted in RAM.
Calls: run_ASCAT.m -> ascat.runAscat -> runASCAT -> [ -> [.data.table
I am aware this is calling a function on the ASCAT package, but I assume this working is essential for CAMDAC.
Do you think it might be an issue with package incompatibility? Do you happen to know a way around it?
I am rerunning the tumour part again printing the session info right before the function above is called, and I will update this with the output as soon as I get it.
Cheers,
Fran
Error in write_fst(df_merged, f_nm) : There was an error creating the file, please check path
Hi there,
I've come across CAMDAC and I was really excited as I think it would be a great resource to analyze our DNA methylation data - I'm particularly interested in using it to call CNVs on the data (thank you and congrats on this really nice work!).
In the first instance I've been trying to run it using the test bam files provided by you on github, to familiarize myself with the tool and its outputs, but it seems like the write_fst() keeps throwing the same error (see issue header). Below, the code I'm running (taken from the available CAMDAC user manual):
CAMDAC::pipeline_tumor_normal(
patient_id="P1",
tumor_id="T",
normal_id="N",
tumor_bam=tumor_bam,
normal_bam=normal_bam,
sex="XY",
path="results/",
pipeline_files="/path/to/pipeline_files_directory",
build="hg38",
min_tumor = 1, # Minimum coverage
min_normal = 10, # Minimum coverage
mq = 0 # Minimum mapping quality
)
I've then tried to modify the get_allele_count() function and replaced write_fst() -> writeRDS() and, despite some warnings, I was able to generate the final output
CHR chrom start end width POS ref alt alt_counts ref_counts total_counts BAF total_depth M UM total_counts_m m CCGG
1 chr1 1 10496 10499 4 NA NA NA NA NA 6 5 1 6 0.8333333 6
2 chr1 1 10505 10505 1 10505 A T 0 6 6 0 6 NA NA NA NA 0
3 chr1 1 10511 10511 1 10511 G A 0 6 6 0 6 NA NA NA NA 0
4 chr1 1 10525 10526 2 NA NA NA NA NA 6 6 0 6 1.0000000 0
5 chr1 1 10539 10539 1 10539 C A 0 6 6 0 6 NA NA NA NA 0
6 chr1 1 10563 10564 2 NA NA NA NA NA 6 6 0 6 1.0000000 0
I've tried several things, but I can't really work out why the write_fst() function wouldn't work - is there anything that I'm missing? I was hoping you might be able to help and advise on this issue?
Thanks so much for your help!
Monica
p.s. below session info
Session info ─────────────────────────────────────────────────────────
setting value
version R version 4.2.2 (2022-10-31)
os macOS Ventura 13.3.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/London
date 2023-05-12
rstudio 2023.03.0+386 Cherry Blossom (desktop)
pandoc NA
Packages
─────────────────────────────────────────────────────────
package * version date (UTC) lib source
ASCAT * 2.5.3 2023-05-12 [1] Github (VanLoo-Lab/ascat@418e1f5)
Biobase * 2.58.0 2022-11-07 [1] Bioconductor
BiocGenerics * 0.44.0 2022-11-07 [1] Bioconductor
BiocParallel 1.32.5 2022-12-25 [1] Bioconductor
Biostrings * 2.66.0 2022-11-07 [1] Bioconductor
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.0)
CAMDAC * 0.1.0 2023-05-12 [1] Github (VanLoo-lab/CAMDAC@287cfd0)
cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.2)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.0)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
curl 5.0.0 2023-01-12 [1] CRAN (R 4.2.0)
data.table * 1.14.6 2022-11-16 [1] CRAN (R 4.2.0)
DelayedArray 0.24.0 2022-11-07 [1] Bioconductor
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
doParallel * 1.0.17 2022-02-07 [1] CRAN (R 4.2.0)
dplyr * 1.1.0 2023-01-29 [1] CRAN (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
foreach * 1.5.2 2022-02-02 [1] CRAN (R 4.2.0)
fs * 1.6.1 2023-02-06 [1] CRAN (R 4.2.0)
fst * 0.9.8 2022-02-08 [1] CRAN (R 4.2.0)
fstcore * 0.9.14 2023-01-12 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
GenomeInfoDb * 1.34.9 2023-02-05 [1] Bioconductor
GenomeInfoDbData 1.2.9 2023-01-16 [1] Bioconductor
GenomicAlignments * 1.34.0 2022-11-07 [1] Bioconductor
GenomicRanges * 1.50.2 2022-12-18 [1] Bioconductor
ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
gridExtra * 2.3 2017-09-09 [1] CRAN (R 4.2.0)
gtable * 0.3.1 2022-09-01 [1] CRAN (R 4.2.0)
hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0)
htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.2.0)
httpuv 1.6.8 2023-01-12 [1] CRAN (R 4.2.0)
IRanges * 2.32.0 2022-11-07 [1] Bioconductor
iterators * 1.0.14 2022-02-05 [1] CRAN (R 4.2.0)
later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.2)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.0)
MatrixGenerics * 1.10.0 2022-11-07 [1] Bioconductor
matrixStats * 0.63.0 2022-11-18 [1] CRAN (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.0)
png * 0.1-8 2022-11-29 [1] CRAN (R 4.2.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.0)
profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.0)
purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0)
RCurl 1.98-1.10 2023-01-27 [1] CRAN (R 4.2.0)
readr * 2.1.3 2022-10-01 [1] CRAN (R 4.2.0)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
rlang 1.1.0 2023-03-14 [1] CRAN (R 4.2.0)
Rsamtools * 2.14.0 2022-11-07 [1] Bioconductor
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
S4Vectors * 0.36.1 2022-12-07 [1] Bioconductor
scales * 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
SummarizedExperiment * 1.28.0 2022-11-07 [1] Bioconductor
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.2.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
XVector * 0.38.0 2022-11-07 [1] Bioconductor
zlibbioc 1.44.0 2022-11-07 [1] Bioconductor
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