dmTest() error in tuQTL analysis
Closed this issue · 1 comments
iaradsouza1 commented
Hi!
I'm performing a tuQLT analysis following the model in DRIMSeq vignette. I formatted my objects to be in the requirements of packages functions and I selected only the SNPs from chromosome 1 just as an example. I'm getting the following error message when I perform the dmTest function:
library(DRIMSeq)
#>
#> Attaching package: 'DRIMSeq'
#> The following object is masked from 'package:base':
#>
#> proportions
# ann = samples df
# genotypes = genotypes df for chr 1 (only SNPs in biallelic sites)
# g_rng = GRange object for gene coordinates in chr 1
# rng = GRange object for SNPs coordinates
# cts = counts df, in scaledTPM
# Build dmSQTL object
w <- 5000
d <- dmSQTLdata(counts = cts, gene_ranges = g_rng,
genotypes = genotypes, snp_ranges = rng,
samples = ann, window = w)
# Filter transcritps
# Get the minimal number of samples where genes should be expressed. I'm using 70% of group samples.
min_samples <- floor(length(ann$sample_id) * 0.7)
d <- dmFilter(d, min_samps_gene_expr = min_samples, min_samps_feature_expr = 5,
minor_allele_freq = 5, min_gene_expr = 10, min_feature_expr = 10)
# get the first 10 genes
d <- d[1:10,]
# Estimate precision
d <- dmPrecision(d)
#> ! Using a subset of 0.1 genes to estimate common precision !
#> ! Using common_precision = 8.1306 as prec_init !
# Fit model
d <- dmFit(d)
# Test
d <- dmTest(d)
#> Error in rbind(deparse.level, ...): numbers of columns of arguments do not matchCreated on 2020-07-14 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.0 (2020-04-24)
#> os Linux Mint 19
#> system x86_64, linux-gnu
#> ui X11
#> language en
#> collate pt_BR.UTF-8
#> ctype pt_BR.UTF-8
#> tz America/Recife
#> date 2020-07-14
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
#> backports 1.1.8 2020-06-17 [1] CRAN (R 4.0.0)
#> BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
#> BiocParallel 1.22.0 2020-04-27 [1] Bioconductor
#> bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
#> callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
#> cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
#> colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
#> devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
#> digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
#> dplyr 1.0.0 2020-05-29 [1] CRAN (R 4.0.0)
#> DRIMSeq * 1.16.0 2020-04-27 [1] Bioconductor
#> edgeR 3.30.3 2020-06-02 [1] Bioconductor
#> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
#> fs 1.4.2 2020-06-30 [1] CRAN (R 4.0.0)
#> generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
#> GenomeInfoDb 1.24.2 2020-06-15 [1] Bioconductor
#> GenomeInfoDbData 1.2.3 2020-07-09 [1] Bioconductor
#> GenomicRanges 1.40.0 2020-04-27 [1] Bioconductor
#> ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.0)
#> glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
#> gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.0)
#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.0)
#> IRanges 2.22.2 2020-05-21 [1] Bioconductor
#> knitr 1.29 2020-06-23 [1] CRAN (R 4.0.0)
#> lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
#> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
#> limma 3.44.3 2020-06-12 [1] Bioconductor
#> locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.0.0)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
#> pillar 1.4.5 2020-07-09 [1] CRAN (R 4.0.0)
#> pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
#> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
#> plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
#> processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.0)
#> ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
#> Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.0)
#> RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0)
#> remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
#> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.0)
#> rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.0)
#> rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.0)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
#> S4Vectors 0.26.1 2020-05-16 [1] Bioconductor
#> scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
#> stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
#> testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
#> tibble 3.0.2 2020-07-07 [1] CRAN (R 4.0.0)
#> tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
#> usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
#> vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.0)
#> withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
#> xfun 0.15 2020-06-21 [1] CRAN (R 4.0.0)
#> XVector 0.28.0 2020-04-27 [1] Bioconductor
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
#> zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
#>
#> [1] /home/iaradsouza/anaconda3/envs/mdd-env/lib/R/libraryMy guess is that Error in rbind(deparse.level, ...): numbers of columns of arguments do not match error happens when dmTest tries to concatenate results with rbind function (see line 257 of https://github.com/gosianow/DRIMSeq/blob/master/R/class_dmSQTLtest.R), since this is an error threw by rbind function when the columns don't match. However, I don't know why this happens.
I tried to encapsulate a minimum example to demonstrate this error, and if you want to reproduce, my data is deposited here: https://github.com/iaradsouza1/drimseq_test.git
I would appreciate any help in this issue, thanks!
gosianow commented
Dear Iara,
thank you very much for reporting this bug and for providing a reproducible example. It was very helpful. The bug should be now fixed in the release version 1.16.1 and in the devel version 1.17.1.
Best wishes.