CheckInputDirFiles: #' Choose the location where 'gene_data' and 'RNAseq_bin'...

In HowardChao/RNA-seq_pipeline:

Description

#' Choose the location where 'gene_data' and 'RNAseq_bin' will be installed #' @export SetPrefixPath <- function(path.prefix = "NOT_SET_YET", print = TRUE) # Check the prefix exist if (isTRUE(dir.exists(path.prefix))) if (substr(path.prefix, nchar(path.prefix), nchar(path.prefix)) != '/') pkg.global.path.prefix$data_path <- paste0(path.prefix, '/') else pkg.global.path.prefix$data_path <- path.prefix if (print) cat(c("************** Setting prefix path ************\n")) cat(paste0("(\u270e) : The following files will be installed under '", pkg.global.path.prefix$data_path, "'\n\n")) return(TRUE) else if (path.prefix == "NOT_SET_YET") stop("(\u2718) Please give value to prefix path.\n\n") return(FALSE) else stop(paste0("(\u2718) Prefix path '", path.prefix, "' is invalid. Please try another one.\n\n")) return(FALSE) #' Checking the absolute path #' @export CheckPrefixPath <- function(path.prefix = pkg.global.path.prefix$data_path, print = TRUE) if (print) cat(c("************** Checking prefix path ************\n")) if (path.prefix == "NOT_SET_YET") stop("(\u2718) You haven't set the prefix directory for the following steps.\n Please run 'SetPrefixPath()' first to set the prefix directory.\n\n") return(FALSE) else if (print) cat(paste0("(\u2714) :Prefix directory: '", pkg.global.path.prefix$data_path, "'\n\n")) return(TRUE) Check input files directory

Usage

CheckInputDirFiles(input.path.prefix = "NOT_SET_YET", gene.name = "NO_DATA",
  sample.pattern = "NO_DATA", print = TRUE)

HowardChao/RNA-seq_pipeline documentation built on May 30, 2019, 11:40 a.m.