qcart: Computes QC-ART scores

In stanfill/QC-ART: Real time quality control of mass spectrometry data

Description

Computes QC-ART scores

Usage

qcart(all_data, baseline, variables, prop = 0.95)

Arguments

all_data	a data frame of all of the data to be analyzed
baseline	vector identifying which rows of 'all_data' are the baseline observations
variables	vector of numbers or column names identifying which columns are the variables to use to compute scores
prop	how many latent variables should be retained? proportion of variability explianed by the latent variables

Value

vector of QC-ART scores corresponding to the rows of 'all_data'

Examples

library(lubridate)
library(QCART)
library(dplyr)
library(ggplot2)

#Load the Amidan et al. (2014) dataset
data("amidan_et_al")  

#Use `lubridate` to  make wokring with time stamps easier
amidan$Acq_Time_Start <- mdy_hm(amidan$Acq_Time_Start)

#Choose one particular instrument to analyze and arrange the rows by time
chosen_inst <- "VOrbiETD04"
vorb_04 <- filter(amidan,Instrument==chosen_inst)
vorb_04 <- arrange(vorb_04,Acq_Time_Start)

#Remove the first 6 rows that occured prior to an instrument cleaning
vorb_04 <- vorb_04[-c(1:6),]

#Choose the variables that will be used to compute QC-ART scores
chosen_vars <- c("P_2C","MS1_Count","MS2_Count","MS1_2B","MS2_1","MS2_2","MS2_3","MS2_4A","MS2_4B","RT_MS_Q1","RT_MS_Q4","RT_MSMS_Q1","RT_MSMS_Q4","XIC_WideFrac")

#Define which observations will be used as the baseline
bline_ob <- 1:50
vorb_04$Baseline <- FALSE
vorb_04$Baseline[bline_ob] <- TRUE

#Compute the scores for that instrument, baseline set and variables
vorb_04$QC_Art <- qcart(all_data = vorb_04, baseline = bline_ob, variables = chosen_vars)

#Plot the scores over time
qplot(Acq_Time_Start,QC_Art,data=vorb_04,colour=Baseline)+xlab("Date")+ylab("QC-ART Score")

stanfill/QC-ART documentation built on May 30, 2019, 9:40 a.m.