Question

adding a description column to glmTreat output

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mictadlo ▴ 10

@mictadlo-10885

Last seen 4.2 years ago

Hi, Below is my current code:

y <- DGEList(counts=rawCountTable, group=group, genes = rownames(rawCountTable))

> head(y$samples)
                        group lib.size norm.factors
X1916.MJO.0001_1 Root_tip.1.5 33986982    0.9543329
X1916.MJO.0002_1 Root_tip.1.5 31781171    0.8787148
X1916.MJO.0003_1 Root_tip.1.5 33947433    0.9948679
X1916.MJO.0004_1 Root_tip.1.5 32704401    1.0003440
X1916.MJO.0005_1   Leaves.1.5 34431708    1.0161298
X1916.MJO.0006_1   Leaves.1.5 33036095    1.0005296

> head(y$genes)
       genes
3  sp0025247
4  sp0025250
5  sp0025268
6  sp0025270
8  sp0025282
12 sp0056834

head(gene.description)
sp0090975    MutS family domain IV2.624413
sp0037632    Magnesium transporter NIPA

How would it be possible to add gene.description column to the below table:

> res <- glmQLFTest(fit, contrast=B.LvsP)
> topTags(res)
Coefficient:  -1*Leaves.2 1*Leaves.3 
          genes     logFC   logCPM        F       PValue          FDR
56010 sp0090975  2.624413 2.847831 374.1120 3.836919e-15 2.262670e-10
73438 sp0037632 -2.984799 3.394748 317.2377 2.065153e-14 5.172707e-10

in order to recieve the following table:

tr <- glmTreat(fit, contrast=B.LvsP, coef = 2, lfc=log2(1.5))
topTags(tr)
Coefficient:  -1*Leaves.2 1*Leaves.3 
          genes    description     logFC   logCPM        F       PValue          FDR
56010 sp0090975    MutS family domain IV2.624413    2.847831 374.1120 3.836919e-15 2.262670e-10
73438 sp0037632    Magnesium transporter NIPA    -2.984799 3.394748 317.2377 2.065153e-14 5.172707e-10

Thank you in advance.

edger • 873 views

ADD COMMENT • link updated 6.5 years ago by Aaron Lun ★ 28k • written 6.5 years ago by mictadlo ▴ 10

score 2 · Accepted Answer · 2017-10-06

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Aaron Lun ★ 28k

@alun

Last seen 2 hours ago

The city by the bay

Just assign gene.description to y$genes at the start of the edgeR analysis (assuming the order of genes/rows is the same between gene.description and rawCountTable, otherwise you will have to reorder the former to match).

ADD COMMENT • link 6.5 years ago Aaron Lun ★ 28k

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Will I lose the gene name column by assign gene.description to y$genes if yes then is there a way to keep both?

ADD REPLY • link 6.5 years ago mictadlo ▴ 10

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Whatever is in y$genes will get cbind'ed to the front of the topTags output. So if you want an extra column of gene names, just add it to y$genes at the beginning our your analysis.

ADD REPLY • link 6.5 years ago Aaron Lun ★ 28k