merge_cells: Storage of intersected factors from multiple cell types as...

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

Description

This function takes the output list of the function "intersect" and stores the intersected value of the factor and annotation files into a dataframe. The values corrsponding to the entries in annotation file represents the corresponding value of in each cell line. If an entry is not found in a factor file, its corresponding value will be 0.

Usage

merge_cells(list, Cells)

Arguments

list	Full path of the file containing name of the Annotations (e.g. gene) in a single column
Cells	output list of function "integrate()"

Value

A dataframe wich rows corresponding to each entry in annotation file and columns corresponding to the intersected value with the corresponding annotation in each cell line.

Author(s)

Subhadeep Das

Examples

anno <- system.file("extdata/annotation2/TSS_groups.bed",
package = "OMICsPCAdata")

fact <- system.file("extdata/factors2/demofactor",
package = "OMICsPCAdata")

Cells <- intersect(fact = fact, anno = anno)

list <- system.file("extdata/annotation2/TSS_list",
package = "OMICsPCAdata")

merged_Cells <- merge_cells(list = list, Cells = Cells)

head(merged_Cells)

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