Merging two plated in R
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0
Entering edit mode
lmrogers34 ▴ 10
@lmrogers34-19639
Last seen 3 days ago
Germany

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
dese DESeq2 • 154 views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

R is case-sensitive. Notice what you have as arguments to DESeqDataSetFromMatrix and what the error says.

0
Entering edit mode

I am an idiot. Thanks. It was driving me mad! That's what I get from copying and pasting code from my old work.

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1
Entering edit mode

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

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