NanoStringNorm (version 1.2.1.1)

read.markup.RCC: read.markup.RCC

Description

A function to read and merge a set of sample specific RCC markup files.

Usage

read.markup.RCC(
 rcc.path = ".",
 rcc.pattern = "*.RCC|*.rcc",
 exclude = NULL, 
 include = NULL,
 nprobes = -1)

Arguments

rcc.path

The directory of the rcc files. Defaults to current working directory.

rcc.pattern

The file pattern used to search for the RCC files. Defaults to the RCC extension

exclude

A list of files to ignore

include

A list of files to include

nprobes

(Optional) This defaults to the read.table default for nrows (-1). In some cases, a message follows the comment ("<") line and causes an error. In this case, the user can now define the number of rows (number of probes including controls and experimental) that should be read in.

Value

Returns a list with two components. The first is the header information which contains sample IDs and diagnostic information on the quality of the samples. The second is the count data and can be directly used in the input to NanoStringNorm.

Examples

# NOT RUN {
# read in all the rcc files in the current directory 
# data.raw <- read.markup.RCC();
# data.norm <- NanoStringNorm(data.raw);

# }