how to create csv file with name of gene from unique ID of lcpm ?
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Björn • 0
@bjorn-12199
Last seen 4.9 years ago
CH

after converting raw counts to cpm from data file using command

lcpm<-cpm(y, log=T)
head(lcpm)

gives first row with unique numeric ID which denotes gene names from data file. How to export name of genes into *.csv file but with name of genes ?

write.csv(highly_variable_lcpm, row.names=y2$genes, file = "highly_variable_lcpm_genes.csv")

I get error message as below

Error in write.table(highly_variable_lcpm, row.names = y2$genes, file = "highly_variable_lcpm_genes.csv", : invalid 'row.names' specification

How to solve the problem ? THx

 

 

edgeR lcpm bioconductor • 994 views
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Aaron Lun ★ 28k
@alun
Last seen 5 hours ago
The city by the bay

Read ?write.csv.

row.names: either a logical value indicating whether the row names of
          ‘x’ are to be written along with ‘x’, or a character vector
          of row names to be written.

The argument needs to be a character vector. y2$genes is a data.frame, hence the error.

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Sorry, still can't find the solution

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Just give the character vector of gene names to write.csv. Presumably the gene names or symbols are stored as a column in y2$genes, so just pull out the relevant column and use that as row.names=.

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I did it as you have said which I have in my first post. 

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If you in an interactive r session do your analysis and type y2$genes you will see that this is not a vector. You hence have to select one of the columns (= a vector) of this dataframe to use as row names.

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