createDataObj-methods: description of function createDataObj

In stela2502/Rscexv: The backend for the SCExV (single cell expression view) server.

description of function createDataObj

Description

This function is the main function used by SCExV. In a script the steps should be executed one by one.

Usage

createDataObj(
  PCR = NULL,
  FACS = NULL,
  max.value = 40,
  ref.genes = NULL,
  max.ct = 25,
  max.control = 0,
  norm.function = "none",
  negContrGenes = NULL,
  use_pass_fail = T,
  ...
)

Arguments

PCR	the pcr data file names default=NULL
FACS	the FACS data file names MISSING default=NULL
max.value	an optional maximum value for all failed wells default=40
ref.genes	if the data should be normalized to reference genes put them into this list
max.ct	all sammples with a ct value of more than max.ct in the ref.genes is dropped
max.control	samples are dropped if 1 (0), 2(1), ... etc ref.genes shows a ct value of more than max.ct
norm.function	any of ( "none","mean control genes","max expression","median expression","quantile" )
negContrGenes	which negative control genes to use (samples with expression there are dropped!)
use_pass_fail	whether or not to use the pass_fail, information in the PCR data files.

stela2502/Rscexv documentation built on July 6, 2022, 9:02 p.m.