Question: cummerbund cuffset filtering to subset or making a significance matrix from a cuffgeneset
gravatar for dtmulder
5.0 years ago by
dtmulder0 wrote:



I'm working with a data set that is missing a lot of data due to quality issues. Therefore many of the transcript FPKM values are scored as 0. As a result, this appears to confound the significance matrix and I end up with thousands of genes marked as significant at alpha=0.05.


What I would like to do is filter the cuffset to exclude those values which are 0 across all samples (rows) or which are 0 in the query sample.


My current approach is a round about way of generating a filtered cuffgeneset but the sigMatrix() function only has an implementation for cuffset objects so I cannot generate the matrix with the cuffgeneset.


My strategy is as follows:


> library(cummeRbund)

> cuff<-readCufflinks()

#get gene matrix for all

> gene.matrix<-fpkmMatrix(genes(cuff))

#score for any row where all values are 0, or query samples are 0

> test <- apply(gene.matrix, 1, function(x) all(x[1:5]==0) | x[7] == 0 | x[11] == 0)

#apply to matrix

> test1 <- gene.matrix[!test,]

#get significantly regulated genes

> mySigGeneIds<-getSig(cuff,alpha=0.05,level='genes')

#get common list of gene names that are significant and where value of query is not 0

> test4 <- Reduce(intersect, list(mySigGeneIds,rownames(test1)))

#build a gene set of those that are significantly regulated and for which we have a value for query

> myGenesSig<-getGenes(cuff,test4)


I'm wondering if you know of a way to apply a filter to the cuffset object to get a subset cuffset instead. Or is there a way to generate a sigmatrix from a cuffgeneset?


Thanks for your time,


rna-seq cummerbund R • 2.3k views
ADD COMMENTlink modified 2.7 years ago by olneykimberly0 • written 5.0 years ago by dtmulder0
gravatar for olneykimberly
2.7 years ago by
olneykimberly0 wrote:

Was this every answered? I would also like to know how to do this. Thank you.

ADD COMMENTlink written 2.7 years ago by olneykimberly0
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