Filtering DGEList object in edgeR
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alakatos ▴ 120
@alakatos-6983
Last seen 3.4 years ago
United States

Hello All, 

I made a DGEList object.

d <- DGEList(counts = COUNTS[,8:43], group = condition,genes=COUNTS$HGNC_symbol) 

 

I added  additional parameters to the list.

rownames(d) <- COUNTS$Ensembl
d$ENTREZ <- COUNTS$NCBI_geneID
d$ENSEMBL <- COUNTS$Ensembl
d$Symbol <- COUNTS$HGNC_symbol
d$length <- COUNTS$Length
d$gc <- COUNTS$GC​

Then I filtered the list.

keep <- rowSums(cpm(d)>2)>= 3
d <- d[keep,]
dim(d)

13980 36

The filtering worked on the original DGEList object but not on the added parameters.

$genes
                   genes
ENSG00000000003   TSPAN6
ENSG00000000419     DPM1
ENSG00000000457    SCYL3
ENSG00000000460 C1orf112
ENSG00000001036    FUCA2
13980 more rows ...

$ENTREZ
[1]  7105 64102  8813 57147 55732
58228 more elements ...

$ENSEMBL
[1] ENSG00000000003 ENSG00000000005 ENSG00000000419 ENSG00000000457 ENSG00000000460
58233 Levels: ENSG00000000003 ENSG00000000005 ENSG00000000419 ENSG00000000457 ... ENSG00000284600
58228 more elements  etc.

I was wondering if there is a way to filter the added parameters as well to keep all the info in one place for downstream analysis.

Thank you for your help and time.

Anita 

DGElist filter edgeR • 2.2k views
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2
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@ryan-c-thompson-5618
Last seen 2.4 years ago
Scripps Research, La Jolla, CA

If you want to add additional gene metadata, do so by adding columns to the d$genes data frame (or creating it if it doesn't exist). Similarly, to add sample metadata, add columns to the d$samples data frame. These elements will be subset along with the counts matrix as you expect.

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It worked. Thanks.

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@gordon-smyth
Last seen 4 minutes ago
WEHI, Melbourne, Australia

As Ryan has already said, you need to add gene annotation columns to d$genes rather than to d itself, for example

d$genes$Symbol <- COUNTS$HGNC_symbol

or perhaps all at once

d$genes <- COUNTS[,1:7]

For more information, type help("DGEList-class")

 

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Thank you.

A

 

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