degMerge: Integrate data comming from degPattern into one data object

In DEGreport: Report of DEG analysis

Description

The simplest case is if you want to convine the pattern profile for gene expression data and proteomic data. It will use the first element as the base for the integration. Then, it will loop through clusters and run degPatterns in the second data set to detect patterns that match this one.

Usage

degMerge(
  matrix_list,
  cluster_list,
  metadata_list,
  summarize = "group",
  time = "time",
  col = "condition",
  scale = TRUE,
  mapping = NULL
)

Arguments

matrix_list	list expression data for each element
cluster_list	list df item from degPattern output
metadata_list	list data.frames from each element with design experiment. Normally colData output
summarize	character column to use to group samples
time	character column to use as x-axes in figures
col	character column to color samples in figures
scale	boolean scale by row expression matrix
mapping	data.frame mapping table in case elements use different ID in the row.names of expression matrix. For instance, when integrating miRNA/mRNA.

Value

A data.frame with information on what genes are in each cluster in all data set, and the correlation value for each pair cluster comparison.

DEGreport documentation built on Nov. 8, 2020, 7:23 p.m.