View source: R/get_list_with_filtered_sites.R
get_list_with_filtered_sites | R Documentation |
Filter phosphorylation sites by extracting all peptides with ion score>=20 and FDR<0.01 from Firmiana and having psites scores.
get_list_with_filtered_sites( peptide_id, files, files_site_score, qc, min_score, min_FDR )
peptide_id |
A vector containing experiment ids as input. |
files |
A data list containing peptides identificaton from Firmiana as input. |
files_site_score |
A data list containing psites scores extracted from mascot xml. The default is NULL, which represents no QC file. |
qc |
A boolean value representing whether it has QC files. The default is True. |
min_score |
A numeric for the minimum score of credible peptides, the default is 20 for Mascot ion score. |
min_FDR |
A numeric for the minimum FDR of credible peptides, the default is 0.01. |
A list containing peptides dataframe with area values and psm, IDs with mergered sequences, gi and sites, new peptides dataframe combined previous peptides dataframe and IDs.
Dongdong Zhan and Mengsha Tong
## Not run: result_list_with_filtered_sites <- get_list_with_filted_sites( peptide.id, files, files_site_score ) ## End(Not run)
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