determine.input: Determine input format

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Description

Determine input format whether its tabular or bed

Usage

determine.input(x, check.chr = FALSE, verbose = TRUE)

Arguments

x	input vector, matrix or dataframe
check.chr	check whether the coordinates are in chromosomal format with chr prefix
verbose	messages and checks

Value

integer value. index format (0), bed (1), index in first column (2), rownmames are index (3), unrecognized(4)

Author(s)

Daryl Waggott

Examples

if (check.binary("bedtools")) {

index <- get.example.regions();
a <- index[[1]];
bedr:::determine.input(a);
}

Example output

######################
#### bedr v1.0.7 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

  * Checking path for bedtools... FAIL

bedr documentation built on May 2, 2019, 11:36 a.m.