search

vdemichev / diann-rpackage

Report processing and protein quantification for MS-based proteomics
Other
32 stars 6 forks source link

Question on output options #3

Closed oliverschilling closed 3 years ago

oliverschilling commented 3 years ago

Dear DIA-NN team

thank you for the fantastic software and the very helpful R-package:

You provide "peptides.maxlfq <- diann_maxlfq(df[df$Q.Value <= 0.01 & df$PG.Q.Value <= 0.01,], group.header="Stripped.Sequence", id.header = "Precursor.Id", quantity.header = "Precursor.Normalised") "

as an example for peptide-level output. Are there other columns that can be added; e.g. gene/potein names (to which a peptide belongs) or preceding / subsequent sequences (i.e. ... similar to MQ-type output)?

Thanks again

Oliver

vdemichev commented 3 years ago

Hi Oliver,

It's not part of the package functionality, but one can easily do that in R. For example,

peptides.maxlfq <- diann_maxlfq(df[df$Q.Value <= 0.01 & df$PG.Q.Value <= 0.01,], group.header="Stripped.Sequence", id.header = "Precursor.Id", quantity.header = "Precursor.Normalised")
gene.names = df$Genes[match(rownames(peptides.maxlfq), df$Stripped.Sequence)]
peptides.maxlfq <- cbind(Genes = gene.names, peptides.maxlfq)

Best wishes,

Vadim