plot_ExpSd_Sig: Plot the stadard deviation against average experssion of...

In YC3/mirNet: microRNA netowrk analyses

Description

plot_ExpSd_Sig plot the standard deviation of genes/microRNAs against their average expression level. With significantly up/down regulated genes/microRNAs highlighted.

Usage

plot_ExpSd_Sig(
  data,
  stat,
  pheno,
  c_fdr = "fdr",
  fdr_cutoff = 0.05,
  c_dir = "logFC",
  c_logFC = "logFC",
  logFC_cutoff = 1,
  filename
)

Arguments

data	A matrix, the normalized gene/microRNA expression dataset, should be a numeric matrix, with rows referring to genes/microRNAs and columns to samples.
stat	The statistic table output from function DoLmFit, pairComp or DoWilcoxonTest.
pheno	A vector of sample phenotypes. Sample phenotype in a scientific research could be treatment/control, normal/cancer or smoker/non-smoker. Different phenotypes should each be encoded as 0/1 when inputting to DoTest, for example, Normal-0; Cancer-1. Currently, only this function accepts two-class pheno data.
c_fdr	The name of the column stores adjusted p-value.
fdr_cutoff	The cutoff of adjusted p-value.
c_dir	The name of the column stores a statistic that is indicative of the direction of alteration.
c_logFC	The name of the column stores log2 fold change.
logFC_cutoff	The cutoff of log2 fold change.
filename	The name of the output figure.

Value

A scatter plot with significant genes/microRNAs highlighted.

See Also

plot_ExpSd

Examples

plot_ExpSd_Sig(data.m, stat, pheno, c_fdr = 'fdr', fdr_cutoff = 0.05, c_dir = 'logFC', c_logFC = 'logFC', logFC_cutoff = 1, filename = 'examples')

YC3/mirNet documentation built on Sept. 3, 2020, 3:25 a.m.