fragment_info: Summary on fragments

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

Summary on fragments

Description

This function outputs a summary on fragments using metrics generated by Picard. Provides the number of mapped fragments, duplication rate and number of unique fragments.

Usage

fragment_info(picard_list)

Arguments

picard_list

Named list of duplication metrics generated by Picard as data frame. Data frames must be named and listed using list(). e.g. list("name1"=file1, "name2"=file2). To import Picard duplication metrics (.txt file) into R as data frame, use picard <- read.table("/path/to/picard/output", header = TRUE, fill = TRUE).

Value

A table summarizing metrics on fragments.

Examples

### Load Data ###
data(CnT_H3K27ac_picard) # example picard output
data(CnR_H3K27ac_picard) # example picard output 
### Import Picard Metrics ###
# To import Picard duplication metrics (.txt file) into R as data frame
# CnT_H3K27ac_picard <- read.table("/path/to/picard/output.txt",
#  header = TRUE,fill = TRUE) 
### Create Named List ###
picard_list <- list("CnT_H3K27ac"=CnT_H3K27ac_picard,
               "CnR_H3K27ac"=CnR_H3K27ac_picard) 
df <- fragment_info(picard_list = picard_list)

neurogenomics/EpiCompare documentation built on Oct. 18, 2024, 11:04 p.m.