meanSDplot: Mean-SD plot

In Vitek-Lab/MSstatsSampleSize: Simulation tool for optimal design of high-dimensional MS-based proteomics experiment

Description

Draw the plot for the mean protein abundance vs standard deviation (square root of variance). The 'lowess' function is used to fit the LOWESS smoother between mean protein abundance and standard deviation.

Usage

meanSDplot(
  data,
  smoother_size = 1,
  xlimUp = 30,
  ylimUp = 3,
  save.pdf = FALSE,
  ...
)

Arguments

data	A list with mean protein abundance vector and standard deviation vector. It should be the output of estimateVar function.
smoother_size	Size of lowess smoother. Default is 1.
xlimUp	The upper limit of x-axis for mean-SD plot. Default is 30.
ylimUp	The upper limit of y-axis for mean-SD plot. Default is 3.
save.pdf	A logical input, determines to save the plots as a pdf or not, the pdf plot is saved in the current working directory, name of the created file is displayed on the console and logged for easier access

Value

meanSDplot is the plot for the mean protein abundance (X-axis) vs standard deviation (Y-axis).

Author(s)

Ting Huang, Meena Choi, Sumedh Sankhe, Olga Vitek

Examples

data(OV_SRM_train)
data(OV_SRM_train_annotation)

variance_estimation <- estimateVar(data = OV_SRM_train,
                                   annotation = OV_SRM_train_annotation)

meanSDplot(variance_estimation)

Vitek-Lab/MSstatsSampleSize documentation built on Aug. 28, 2020, 10:39 a.m.