stagingByTranscription: stagingByTranscription

In foster-gabe/PFExpTools: Tools for analysis of Plasmodium falciparum gene expression data

Description

This function compares each whole transcriptome sample to every time point in the provided reference time course, and identifies the best time point fit. Correlation is determined by the Pearson method.

Usage

stagingByTranscription(
  samples,
  reference,
  subset = NA,
  cortable = F,
  heatmap = T,
  start = 1
)

Arguments

samples	A matrix of expression samples, with rows as genes and columns as samples. This is the set that will be tested.
reference	A reference expression time course, with rows as genes and columns as samples.
subset	The default is to use all genes in common between the two sets; if a subset is desired, provide this as vector of gene names in the subset.
cortable	If the full matrix of correlation values is desired, set to TRUE; default is FALSE.
heatmap	A simple correlation heatmap will be generated as default. Set to false to skip.
start	What hour the reference course starts at- default is 1hpi

Value

Default return is a matrix with one column; rows are samples and values are the time point of maximum correlation. The function will also plot a simple heatmap by default. If cortable is set to TRUE, the function will return a list; the first entry is the simple time point matrix, and the second entry is the full correlation matrix.

foster-gabe/PFExpTools documentation built on May 25, 2020, 7:22 a.m.