Use all factors as phenoData for XCMS

[sneumann]

Hi,

Currently, processAssayXcmsSet() will obtain the first factor from the ISAtab
and use it as sampclass() for the xcmsSet. It would be great if all factors were used.
Below is an example.

Yours,
Steffen

# Create a data.frame with one column per factor
phenodataMtbls2 <- cbind(genotype=c("Col-0", "Col-0", "Col-0", "Col-0", "cyp79", "cyp79", "cyp79",  "cyp79", "Col-0", "Col-0", "Col-0", "Col-0", "cyp79", "cyp79",  "cyp79", "cyp79"), replicate=rep(c("Exp1", "Exp2"), each=8))

# add the assay names as rownames
rownames(phenodataMtbls2) <- c("MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818", "MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820",  "MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822", "MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824",  "MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819", "MSpos-Ex1-cyp79-48h-Ag-2_1-B,2_01_9821",  "MSpos-Ex1-cyp79-48h-Ag-3_1-B,1_01_9823", "MSpos-Ex1-cyp79-48h-Ag-4_1-B,2_01_9825",  "MSpos-Ex2-Col0-48h-Ag-1_1-A,2_01_9827", "MSpos-Ex2-Col0-48h-Ag-2_1-A,3_01_9829",  "MSpos-Ex2-Col0-48h-Ag-3_1-A,4_01_9831", "MSpos-Ex2-Col0-48h-Ag-4_1-A,2_01_9833",  "MSpos-Ex2-cyp79-48h-Ag-1_1-B,3_01_9828", "MSpos-Ex2-cyp79-48h-Ag-2_1-B,4_01_9830",  "MSpos-Ex2-cyp79-48h-Ag-3_1-B,3_01_9832", "MSpos-Ex2-cyp79-48h-Ag-4_1-B,4_01_9834" )

# Assign to phenoData sloe in xcmsSet
phenoData(mtblsSet) <- phenodataMtbls2

# As you see, each assay file has its catenation of factors as sampclass().
sampclass(mtblsSet )
 [1] Col-0.Exp1 Col-0.Exp1 Col-0.Exp1 Col-0.Exp1 cyp79.Exp1 cyp79.Exp1
 [7] cyp79.Exp1 cyp79.Exp1 Col-0.Exp2 Col-0.Exp2 Col-0.Exp2 Col-0.Exp2
[13] cyp79.Exp2 cyp79.Exp2 cyp79.Exp2 cyp79.Exp2
Levels: Col-0.Exp1 cyp79.Exp1 Col-0.Exp2 cyp79.Exp2

[agbeltran]

For the step 2

# add the assay names as rownames

it should be

# add the 'raw spectral data files' as rownames