preprocess MQ peptide
Description
preprocess MQ peptide
Usage
preprocess_MQ_peptide(
quant_data,
fasta_file,
annotation,
pattern_contaminants = "^zz|^CON|Cont_",
pattern_decoys = "^REV_|^rev_",
hierarchy_depth = 1,
nr_peptides = 1
)
Arguments
quant_data
|
path to peptides.txt file |
fasta_file
|
path to fasta file(s) |
annotation
|
annotation list from read_annotation |
pattern_contaminants
|
regex pattern for contaminants |
pattern_decoys
|
regex pattern for decoys |
hierarchy_depth
|
hierarchy depth for aggregation |
nr_peptides
|
minimum number of distinct (stripped) peptides per protein (>= 1, default 1) |
Value
A list containing the prepared LFQData and ProteinAnnotation objects.