Common Use Tools for Genomic Analysis.

HodgesTools

Overview

HodgesTools is an R package built by hodges lab members for current and future hodges lab members as well as anyone else who might find the tools useful. This package contains functions that the lab uses everyday to analyze various genomic datasets. Critically, this package only contains general use functions; functions specific to a given technique are reserved for a separate package. As the lab grows, we expect to continue adding functions to the package to build on previous lab members code.

Examples

Below is an example for the read_bed function.

read_bed

The read_bed function reads a tab-delimited BED formatted file into R. It auto-detects BED3, BED6, BED3+, and BED6+ formats. Below is an example for a BED6 file.

# load package
devtools::load_all() #this is development code, use library(HodgesTools)
#> i Loading HodgesTools

#load data from extdata directory
BED6 <- system.file(package = "HodgesTools", "extdata", "test_BED6.bed")

#read 6 column bedfile into R
bed6 <- read_bed(BED6)
#> User-supplied file read as 6-column BED.
head(bed6)
#> # A tibble: 4 x 6
#>   chr   start   end name  score strand
#>   <chr> <dbl> <dbl> <chr> <dbl> <chr> 
#> 1 chr1    123   456 NAME1   123 .     
#> 2 chr1    789  1908 NAME2   123 -     
#> 3 chr1   1789  2908 NAME3   123 +     
#> 4 chr1   3789  3908 NAME4   123 -

Installation

This package can be installed via CRAN:

install.packages('HodgesTools')

Tools

The following functions are provided in this release:

• read_bed
• plot_HOMERTFs
• cpg_analysis
• createManhattandQQ
• append_section_to_ini

Note: Usage and arguments for each function can be viewed in the manual.