Entering edit mode
I am trying to merge two plates together in R. I have merged the plates and dropped rows as below. However, it keeps giving me this error message
"error in evaluating the argument 'x' in selecting a method for function 'ncol': argument "countData" is missing, with no default"
However, I can do ncol on my data just fine. I am not sure what is going on. Does anyone have any ideas?
countdata.P1=read.csv("all.p1.count", sep="", head=T, skip=1, row.names = "Geneid") # ignores first line
rawdata.P1=countdata.P1
# Clean file names
colnames(countdata.P1) <- gsub("\\.Aligned.sortedByCoord.out.bam", "_p1", colnames(countdata.P1))
colnames(countdata.P1) <- gsub("X.media.hard.drive3.TropI.scRNA_HIV.mapping.", "", colnames(countdata.P1))
countdata.P1 <- countdata.P1[ ,7:ncol(countdata.P1)] ## removing meta data
# Drop empty table, H12, renamed at read stage
countdata.P1 <- subset(countdata.P1, select=-c(H12_p1, G05_p1)) # Remove Row H12, empty sample, and G05 - not enough counts
write.table(countdata.P1, "counts_cleaned.txt", sep="\t", row.names=FALSE, quote=FALSE)
rna.metadata.P1 <- read.csv("metadata.p1.tab",sep = "\t", header = TRUE, row.names=1)
rna.metadata.P1 <- rna.metadata.P1[!(row.names(rna.metadata.P1) %in% c("G05")), ]
coldata.p1 <- data.frame(row.names=colnames(countdata.P1), rna.metadata.P1)
## Plate 2
countdata.p2=read.csv("all.p2.count", sep="", head=T, skip=1, row.names = "Geneid") # ignores first line
rawdata.p2=countdata.p2
# Clean file names
colnames(countdata.p2) <- gsub("\\_.fq.Aligned.sortedByCoord.out.bam", "_p2", colnames(countdata.p2))
colnames(countdata.p2) <- gsub("X.media.hard.drive3.TropI.scRNA_HIV.2020_12_17_reads.mapping.", "", colnames(countdata.p2))
countdata.p2 <- countdata.p2[ ,7:ncol(countdata.p2)] ## removing meta data
countdata.p2 <- subset(countdata.p2, select=-c(H12_p2)) # Remove Row H12, empty sample, and G05 - not enough counts
# Drop empty table, H12, renamed at read stage
write.table(countdata.p2, "counts_cleaned.txt", sep="\t", row.names=FALSE, quote=FALSE)
rna.metadata.p2 <- read.csv("metadata.p2.tab",sep = "\t", header = TRUE, row.names=1)
rna.metadata.p2 <- rna.metadata.p2[!(row.names(rna.metadata.p2) %in% c("p2_D4")), ]
coldata.p2 <- data.frame(row.names=colnames(countdata.p2), rna.metadata.p2)
coldata <- rbind(coldata.p1, coldata.p2)
countdata <- merge(countdata.P1, countdata.p2, by=0)
dds_poscounts <- DESeqDataSetFromMatrix(countdata=as.matrix(countdata), colData=coldata, design=~plate + group)
sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_IE.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_IE.UTF-8
[6] LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_IE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] pheatmap_1.0.12 ggrepel_0.9.1 tibble_3.1.7 dplyr_1.0.9
[5] ggplot2_3.3.6 DESeq2_1.36.0 SummarizedExperiment_1.26.1 Biobase_2.56.0
[9] MatrixGenerics_1.8.0 matrixStats_0.62.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.1
[13] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] locfit_1.5-9.5 Rcpp_1.0.8.3 lattice_0.20-45 png_0.1-7 Biostrings_2.64.0 assertthat_0.2.1
[7] utf8_1.2.2 R6_2.5.1 RSQLite_2.2.13 httr_1.4.3 pillar_1.7.0 zlibbioc_1.42.0
[13] rlang_1.0.2 rstudioapi_0.13 annotate_1.74.0 blob_1.2.3 Matrix_1.4-1 splines_4.2.0
[19] BiocParallel_1.30.0 geneplotter_1.74.0 RCurl_1.98-1.6 bit_4.0.4 munsell_0.5.0 DelayedArray_0.22.0
[25] compiler_4.2.0 pkgconfig_2.0.3 tidyselect_1.1.2 KEGGREST_1.36.0 GenomeInfoDbData_1.2.8 XML_3.99-0.9
[31] fansi_1.0.3 withr_2.5.0 crayon_1.5.1 bitops_1.0-7 grid_4.2.0 xtable_1.8-4
[37] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.3 scales_1.2.0 cli_3.3.0
[43] cachem_1.0.6 XVector_0.36.0 genefilter_1.78.0 ellipsis_0.3.2 vctrs_0.4.1 generics_0.1.2
[49] RColorBrewer_1.1-3 tools_4.2.0 bit64_4.0.5 glue_1.6.2 purrr_0.3.4 parallel_4.2.0
[55] fastmap_1.1.0 survival_3.3-1 AnnotationDbi_1.58.0 colorspace_2.0-3 memoise_2.0.1
I am an idiot. Thanks. It was driving me mad! That's what I get from copying and pasting code from my old work.
Heh. I know how you feel. Can't tell you how many times I've sat here staring at some code thinking 'why does this not work!?!' I blame R, mostly. ;-D