CODEWITHSUNDEEP
rbioinformaticssequencing
Aranyak Goswami
Aranyak Goswami

Reputation: 19

Script out of bounds in R

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,]

Upvotes: 0

Views: 424

Answers (1)

jared_mamrot
jared_mamrot

Reputation: 26695

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.

Upvotes: 0

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