readAgilent: Read agilent files

In AlexeiSleptcov/aggi: Agilent arrays analisys (aggy)

Description

Read Feature Extraction's txt files.

Usage

readAgilent(targets = NULL, path = getwd(), format = c("C", "F"),
  dyes = 2, collect = c("proc", "median", "mean", "lr", "dn"),
  verbose = 0)

Arguments

targets	Feature Extraction's files. TXT format files only.
path	filepath, where FE-files are stored. Default: getwd().
format	which format your FE-files have? Default: "compact"
collect	what the data signals you want to process? Default: "processed".
macolors	read two-color (2) or one-color (1) microarray.

Details

Collecting data from the format "compact" can be taken on the processed signals ("processed"), raw data ("mean" or "median") or LogRatio ("LogRatio"). At the same time, if format selected as "full" you may collect normalized data ("DyeNorm").

Targets object must be class data.frame, and have two required column name (eg.: "array1", "array2") and filenames (eg. "2802860_12158125.txt").

Value

Read Feature Extraction's files.

See Also

readGenePix

Examples

# targets <- read.table("targets.txt", header = TRUE, stringsAsFactors = FALSE)
# MyArrays <- readAgilent(targets, collect = "median")

AlexeiSleptcov/aggi documentation built on May 5, 2019, 4:53 a.m.