View source: R/Canidate_processing.R
Protein_feature_list_fun | R Documentation |
This is a function that prepare the candiate list for maldi imaging data qualitative or quantitative analysis.
this function will read the fasta file and generate mz for the adducts list defined in "adducts"
.
Protein_feature_list_fun(
workdir = getwd(),
database,
Digestion_site = "[G]",
missedCleavages = 0:1,
Multiple_mode = c("sequential", "parallel"),
adducts = c("M+H", "M+NH4", "M+Na"),
BPPARAM = bpparam(),
Decoy_search = T,
Decoy_mode = c("adducts", "elements", "isotope", "sequence"),
Decoy_adducts = c("M+He", "M+Ne", "M+Ar", "M+Kr", "M+Xe", "M+Rn"),
Substitute_AA = list(AA = c(NULL), AA_new_formula = c(NULL), Formula_with_water =
c(NULL)),
mzrange = c(500, 4000),
output_candidatelist = T,
Modifications = list(fixed = NULL, fixmod_position = NULL, variable = NULL,
varmod_position = NULL),
use_previous_candidates = F,
Protein_desc_of_exclusion = NULL,
Database_stats = F
)
workdir |
the folder that contains fasta file |
database |
the file name of fasta file |
Digestion_site |
Digestion pattern, this is the |
missedCleavages |
Define a number range for misscleaved peptides to be considered |
adducts |
the adducts list to be used for generating the PMF search candidates |
BPPARAM |
parallel processing parameter for BiocParallel |
a table of peptide candiate list
Protein_feature_list_fun(database="lipid candidates.csv",adducts=c("M+H","M+NH4","M+Na"))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.