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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.
Below is an example for the read_bed function.
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 -This package can be installed via CRAN:
install.packages('HodgesTools')The following functions are provided in this release:
Note: Usage and arguments for each function can be viewed in the manual.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.