filter_Ct {RQdeltaCT}

filter_Ct

Description

This function filters Ct data according to the used filtering criteria (see parameters).

Usage

filter_Ct(
  data,
  flag.Ct = "Undetermined",
  maxCt = 35,
  flag = c("Undetermined"),
  remove.Gene = c(""),
  remove.Sample = c(""),
  remove.Group = c("")
)

Arguments

data

Object returned from read_Ct_long() or read_Ct_wide() function, or data frame containing column named "Sample" with sample names, column named "Gene" with gene names, column named "Ct" with raw Ct values, column named "Group" with group names. Optionally, data frame can contain column named "Flag" with flag information (e.g. "Undetermined" and "OK"), which will be used for filtering.

flag.Ct

Character of a flag used for undetermined Ct values, default to "Undetermined".

maxCt

Numeric, a maximum of Ct value allowed.

flag

Character: flag used in Flag column for values which should be filtered out, default to "Undetermined".

remove.Gene

Character: vector with names of genes to remove from data

remove.Sample

Character: vector with names of samples to remove from data

remove.Group

Character: vector with names of groups to remove from data

Value

Data frame with filtered data.

Examples

library(tidyverse)
data(data.Ct)
data.CtF <- filter_Ct(data.Ct,
                      remove.Gene = c("Gene2","Gene5","Gene6","Gene9","Gene11"),
                      remove.Sample = c("Control08","Control16","Control22"))

dim(data.Ct)
dim(data.CtF)