descriptor: Distribution of Assays as percentage of cell lines

In OMICsPCA: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

Description

descriptor() produces panels of boxplots displaying the distribution of various factors(e.g. ChIP-seq of H3k9ac histone modification) in percentage of cell lines.

choice = 1 output is collection of boxplots explaining the distribution of percentage of cell lines having or overlapping with the input factors (e.g. H3k9ac).

choice = 2 displays the distribution of percentage of cell lines having or overlapping with increasing number of factors for the selected group (e.g. WE or RE etc). If this option is selected, then a group name should be provided through choice2group.

Usage

descriptor(name, factors, groups,
choice = 1, choice2group = NULL, title = NULL,
groupinfo = NULL)

Arguments

name	Name of the "MultiAssayExperiment" object containing the assay data
factors	A vector containing the name of the Assays
groups	Name of all or subset of groups
choice	Numerical value between 1 and 2. See Description and vignettes for details of plots generated by this 2 choices
choice2group	Used when choice is 2. This argument allows a name of group.
title	Title of the plot
groupinfo	output of create_group() or similar object

Value

Displays various plots as per the combination of various input arguments.

Author(s)

Subhadeep Das <[e-mail]>

Examples

descriptor(name = multi_assay,
factors = c(
"H2az","H3k9ac","H3k4me1"),
groups = c("WE","RE","IntE","NE"),
choice = 1,
title = "Distribution of percentage of cell types overlapping
with various factors",
groupinfo = groupinfo_ext)

OMICsPCA documentation built on Nov. 8, 2020, 5:01 p.m.