annot_KinSub: Annotates kinase-substrate interactions

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

Annotates kinase-substrate interactions

Description

Annotates kinase-substrate interactions

Usage

annot_KinSub(df, db_nms, match_orgs, id, 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 PSP database(s) with prepended directory path(s). Users need to download the kinase-substrate table, e.g. Kinase_Substrate_Dataset.txt directly from the PSP website and supply the corresponding file path(s) and name(s). Currently assume single database file.
match_orgs	Logical; if TRUE, matches the organism between kinases and their acting substrates. The default is TRUE.
id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
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 of data against the column keys in Peptide.txt for peptides or Protein.txt for proteins. Each statement contains to a list of logical expression(s). The lhs needs to start with filter_. The logical condition(s) at the rhs needs to be enclosed in exprs with round parenthesis. For example, pep_len is a column key in Peptide.txt. The statement filter_peps_at = exprs(pep_len <= 50) will remove peptide entries with pep_len > 50. See also normPSM. Additional parameters for plotting with ggplot2: xmin, the minimum x at a log2 scale; the default is -2. xmax, the maximum x at a log2 scale; the default is +2. xbreaks, the breaks in x-axis at a log2 scale; the default is 1. binwidth, the binwidth of log2FC; the default is (xmax - xmin)/80. ncol, the number of columns; the default is 1. width, the width of plot; height, the height of plot. scales, should the scales be fixed across panels; the default is "fixed" and the alternative is "free".

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.