Closed Ziwei-Liu closed 1 year ago
My code are as follow:
library(methylKit) file.list2=list("/media/user/02_analysis/methylation/04_methylkit/N_K-1/N_K-1_CG_methylkit.txt","/media/user/02_analysis/methylation/04_methylkit/N_K-2/N_K-2_CG_methylkit.txt","/media/user/02_analysis/methylation/04_methylkit/N_K-3/N_K-3_CG_methylkit.txt","/media/user/02_analysis/methylation/04_methylkit/N_G-1/N_G-1_CG_methylkit.txt","/media/user/02_analysis/methylation/04_methylkit/N_G-2/N_G-2_CG_methylkit.txt","/media/user/02_analysis/methylation/04_methylkit/N_G-3/N_G-3_CG_methylkit.txt") myobj=methRead(file.list2,sample.id=list("N_K-1","N_K-2","N_K-3","N_G-1","N_G-2","N_G-3"),treatment=c(1,1,1,0,0,0),context="CpG")
and then R reported errors as follow:
Received list of locations. Error in if (is.na(treatment)) stop("Treatment vector is missing.") : the condition has length > 1
I completely followed the user guide, but bugs happened. Please tell me how to fix it.
My system Info:
R version 4.3.0 (2023-04-21) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS Matrix products: default BLAS/LAPACK: /media/local/conda/miniconda3/envs/R4.3.0/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0 other attached packages: [1] ggplot2_3.4.3 methylKit_1.26.0 GenomicRanges_1.52.0 [4] GenomeInfoDb_1.36.2 IRanges_2.34.1 S4Vectors_0.38.1 [7] BiocGenerics_0.46.0
It works after I added the missing "assembly" argument. Problem fixed.
My code are as follow:
and then R reported errors as follow:
I completely followed the user guide, but bugs happened. Please tell me how to fix it.
My system Info: