annot_stringdb: Annotates protein STRING ids

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Annotates protein STRING ids

Description

Annotates protein STRING ids

Usage

annot_stringdb(
  df,
  db_nms,
  id,
  score_cutoff,
  filepath = NULL,
  filename = NULL,
  ...
)

Arguments

df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
db_nms	Character string(s) to the name(s) of STRING database(s) with prepended directory path. The STRING database(s) need to match those generated from prepString. There is no default and users need to provide the correct file path(s) and name(s).
id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
score_cutoff	Numeric; the threshold in the combined_score of protein-protein interaction. The default is 0.7.
filepath	A file path to output results. By default, it will be determined automatically by the name of the calling function and the value of id in the call.
filename	A representative file name to outputs. By default, the name(s) will be determined automatically. For text files, a typical file extension is .txt. For image files, they are typically saved via ggsave or pheatmap where the image type will be determined by the extension of the file name.
...	filter_: Variable argument statements for the row filtration against data in a primary file linked to df. See also normPSM for the format of filter_ statements. arrange_: Variable argument statements for the row ordering against data in a primary file linked to df. See also prnHM for the format of arrange_ statements.

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.