Loading Traitdata file for WGCNA analysis
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9 weeks ago
priya.bmg ▴ 40

Hello

I am trying to load the trait data for WGCNA analysis. I followed the steps given in section 1c of this link https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-01-dataInput.pdf. I have a problem in loading the traitdata. Has anyone come across this error

I have 492 rows as samples

traitData = read.csv("F:\\gene_priortization\\wgcnafiles\\trait.csv")
allTraits = traitData[c(1:2)] ## select the first two columns. First column has 492 sample names and second column is coded 1 or 2
dim(allTraits)
names(allTraits)

Samples = rownames(df1_edit_cg); ##df1_edit_cg is the expression data 
traitRows = match(Samples, allTraits$ArrayName); ##I get a list with 492 integers
datTraits = allTraits[traitRows, -1]; ## Here I get the second column from all traits coded as 1 or 2
rownames(datTraits) = allTraits[traitRows, 1];

Error in `rownames<-`(`*tmp*`, value = c("X8.pcw_amygdaloid.complex",  : 
  attempt to set 'rownames' on an object with no dimensions


datTraits
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
 [57] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[113] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[169] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[225] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[281] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[337] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[393] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[449] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

Thanks

loading trait file WGCNA • 274 views
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Please provide an example of datTraits, it is likely impossible to help without seeing data head(datTraits)

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I have given an example of datTrait in the question above

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Well datTraits is a vector, it is not a dataframe. If you want to give names to a vector you need names(datTraits)= ...

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Thank you

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