prepFml: Prepare formulas

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

Prepare formulas

Description

Prepare formulas

Usage

prepFml(formula, label_scheme_sub, ...)

Arguments

formula	Language; the formula in linear modeling.
label_scheme_sub	A data frame. Subset entries from label_scheme for selected samples.
...	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 Dec. 14, 2024, 12:27 p.m.