Question

How to create a matrix from a set of files containing counts for a set of attributes?

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jdanowski • 0

@jdanowski-23686

Last seen 4.6 years ago

I have a set of files, one for each African country, that contain online news themes. https://drive.google.com/drive/folders/1nJvLwVDAdaMhRqTDMP6bP8sU8lgKLT1Y?usp=sharing

I would like to create a matrix where each row is a country and the columns are the aggregate themes.

The package "edgeR" that looks like it will do this. When I install it and try to run the function "readDGE" to produce the matrix I get errors. Here is the function:

readDGE(files, path=NULL, columns=c(1,2), group=NULL, labels=NULL, ...)

Error: Error: '...' used in an incorrect context

I tried it without the ellipsis and got this: Error in is.data.frame(files) : object 'files' not found

How can I get this working? Or, is there a better way to create the matrix in another package?

edgeR • 1.6k views

ADD COMMENT • link updated 4.6 years ago by Gordon Smyth 52k • written 4.6 years ago by jdanowski • 0

score 2 · Accepted Answer · 2020-06-13

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Gordon Smyth 52k

@gordon-smyth

Last seen 28 minutes ago

WEHI, Melbourne, Australia

You have to create a vector of file names.

myfilenames <- c("myfile1", "myfile2")
y <- readDGE(files = myfilenames)

Note of course you have adapt my example to your files, not just copy my code.

ADD COMMENT • link 4.6 years ago Gordon Smyth 52k

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Thank you for your help, Gordon!

ADD REPLY • link 4.6 years ago jdanowski • 0

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To output the matrix, I wrote: write.csv(y)
But, I get a warning:
Warning message: In (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : row names were found from a short variable and have been discarded

ADD REPLY • link 4.6 years ago jdanowski • 0

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Update: I entered all of my files (n=38). When specifying: write.csv(y) I get this error: write.csv(y) Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : arguments imply differing number of rows: 38, 1442

ADD REPLY • link 4.6 years ago jdanowski • 0

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You should get into the habit of understanding the structure and class of your objects. For example, try this:

class(y)
str(y)

It should be a DGEList object, so, not a data-matrix or data-frame as you expect. This means that write.csv() will not know what to do with it. Gordon has already solved the initial issue. To solve any other related issues, I really encourage you to first go through the EdgeR workflow / vignette / user's guide so that you better understand how to use the package.

PS - the data that you probably want is stored in the counts variable, so, accessible via y$counts; however, these will not be normalised for size factors.

ADD REPLY • link 4.6 years ago Kevin Blighe ★ 4.0k

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Thank you for your advice!

ADD REPLY • link 4.6 years ago jdanowski • 0

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Another attempt:

write.csv(y,"C:/Users/james/Desktop/Documents/Downloads/txtfiles/ICTThemesMatrix.csv", row.names = T)

Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : arguments imply differing number of rows: 38, 1442

ADD REPLY • link 4.6 years ago jdanowski • 0