pep quantification #29
Description
Hi, Thang,
I‘m processing “report.tsv” from DIA-NN, except protein quantification. Is iq also avaliable for peptide quantification as following code:
iq::process_long_format(file.path(file="report.tsv"),
output_filename = "pep_iqfiltered.tsv",
sample_id = "Run",
primary_id = "Stripped.Sequence",
filter_double_less = c("Lib.Q.Value" = "0.01", "Lib.PG.Q.Value" = "0.01"),
annotation_col = c("Protein.Names", "Genes"),
intensity_col = "Precursor.Normalised",
show_boxplot = F
,peptide_extractor = function(x) gsub("[0-9].*$", "", x)
)
Additionally, I have used following code in the past but to find_peptide_type I could't close filter of proteotypic with "filter_string_equal = c("Proteotypic" = c("1", "0"))".
iq_dat <- iq::fast_read(file.path(file="report_pep.tsv"),
sample_id = "Run",
primary_id = "Stripped.Sequence",
secondary_id = c("Precursor.Id"),
intensity_col = "Precursor.Normalised",
annotation_col = c("Protein.Names", "Genes"),
filter_double_less = c("Lib.Q.Value" = "0.01", "Lib.PG.Q.Value" = "0.01"),
filter_string_equal = c("Proteotypic" = "1"))
Thanks,
Zoe