Script out of bounds in R - r

Question

I am using a code based on Deseq2. One of my goals is to plot a heatmap of data.
heatmap.data <- counts(dds)[topGenes,]
The error I am getting is
Error in counts(dds)[topGenes, ]: subscript out of bounds
the first few line sof my counts(dds) function looks like this.
99h1 99h2 99h3 99h4 wth1 wth2
ENSDARG00000000002 243 196 187 117 91 96
ENSDARG00000000018 42 55 53 32 48 48
ENSDARG00000000019 91 91 108 64 95 94
ENSDARG00000000068 3 10 10 10 30 21
ENSDARG00000000069 55 47 43 53 51 30
ENSDARG00000000086 46 26 36 18 37 29
ENSDARG00000000103 301 289 289 199 347 386
ENSDARG00000000151 18 19 17 14 22 19
ENSDARG00000000161 16 17 9 19 10 20
ENSDARG00000000175 10 9 10 6 16 12
ENSDARG00000000183 12 8 15 11 8 9
ENSDARG00000000189 16 17 13 10 13 21
ENSDARG00000000212 227 208 259 234 78 69
ENSDARG00000000229 68 72 95 44 71 64
ENSDARG00000000241 71 92 67 76 88 74
ENSDARG00000000324 11 9 6 2 8 9
ENSDARG00000000370 12 5 7 8 0 5
ENSDARG00000000394 390 356 339 283 313 286
ENSDARG00000000423 0 0 2 2 7 1
ENSDARG00000000442 1 1 0 0 1 1
ENSDARG00000000472 16 8 3 5 7 8
ENSDARG00000000476 2 1 2 4 6 3
ENSDARG00000000489 221 203 169 144 84 114
ENSDARG00000000503 133 118 139 89 91 112
ENSDARG00000000529 31 25 17 26 15 24
ENSDARG00000000540 25 17 17 10 28 19
ENSDARG00000000542 15 9 9 6 15 12
How do I ensure all the elements of the top genes are present in it?
When I try to see 20 top genes in the dataset. it looks like a list of genes
6339" "12416" "1241" "3025" "12791" "846" "15090"
[8] "6529" "14564" "4863" "12777" "1122" "7454" "13716"
[15] "5790" "3328" "1231" "13734" "2797" "9072" with the column head V1.
I have used both
topGenes <- read.table("E://mir99h50 Cheng data//topGenesresordered.txt",header = TRUE)
and
topGenes <- read.table("E://mir99h50 Cheng data//topGenesresordered.txt",header = FALSE)
to see if the out of bounds error is removed. However it was of no use. I guess the V1 head is causing the issue.
The top genes function has been generated using the above code snippet.
resordered <- res[order(res$padj),]
#Reorder gene list by increasing pAdj
resordered <- as.data.frame(res[order(res$padj),])
#Filter for genes that are differentially expressed with an FDR < 0.01
ii <- which(res$padj < 0.01)
length(ii)
# Use the rownames() function to get the top 20 differentially expressed genes from our results table
topGenes <- rownames(resordered[1:20,])
topGenes
# Get the counts from the DESeqDataSet using the counts() function
heatmap.data <- counts(dds)[topGenes,]

Answer 1

Perhaps this will do what you want?
counts_dds <- counts(dds)
topgenes <- c("ENSDARG00000000002", "ENSDARG00000000489", "ENSDARG00000000503",
"ENSDARG00000000540", "ENSDARG00000000529", "ENSDARG00000000542")
heatmap.data <- counts_dds[rownames(counts_dds) %in% topgenes,]
If you provide more information it will be easier to advise you on how to fix your problem.