pooledpeaks (version 1.1.1)

fsa_batch_imp: Batch Import of .fsa files

Description

This function imports and extracts all of the information out of the .fsa files and combines them into one list type object.fsa_batch_imp is a modification of the original Fragman import script function, storing.inds, This revised script accommodates ABI's .fsa file format up to version 3. It retains Fragman functions for Fourier transformation, saturated peaks, and pull-up correction. Notable adjustments include updating channel parameters, utilizing Dyechannel count from the file directory, and streamlining the script by extracting data only from "DATA" tags. Major changes involve column selection for v3 formats and modifications to the "channel" parameter. Minor changes include allowing relative paths for the data directory, importing only .fsa files, and renaming channels with dye names. This revision ensures successful execution for any format version up to 3.

Usage

fsa_batch_imp(
  folder,
  channels = NULL,
  fourier = TRUE,
  saturated = TRUE,
  lets.pullup = FALSE,
  plotting = FALSE,
  rawPlot = FALSE,
  llength = 3000,
  ulength = 80000
)

Value

Output is a LIST where each element of the list is a DATAFRAME with the channels in columns for each FSA file

Arguments

folder

The path to the folder from the current directory where the .fsa files that will be analyzed are stored.

channels

The number of dye channels expected, including the ladder.

fourier

True/False Should fourier transformation be applied.

saturated

True/False whether to Check and correct for saturated peaks.

lets.pullup

True/False Applying pull up correction to the samples to decrease noise from channel to channel. The default is FALSE, please do not change this.

plotting

True/False Should plots be drawn of all channels after data cleaning.

rawPlot

True/False indicating whether a plot should be drawn of all vectors.

llength

A numeric value for the minimum number of indexes in each channel.

ulength

A numeric value for the maximum number fo indexes in each channel.

Examples

file_path <- system.file("extdata", package = "pooledpeaks")
fsa_batch_imp(file_path, channels = 5, fourier = FALSE, saturated = FALSE ,
lets.pullup = FALSE,plotting = FALSE, rawPlot = FALSE)