compute_threshold: Computes threshold values for QC-ART Scores

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

Description

This function will compute threshold values for QC-ART scores computed using the 'qcart' function.

Usage

compute_threshold(scores, baseline, time_stamps, type = "static",
  perc = 0.95)

Arguments

scores	the QC-ART scores returned by 'qcart'
baseline	a vector of logical values (TRUE/FALSE) indicating which observations were used as the baseline
time_stamps	the vector of time stamps assocaited with the QC-ART scores
type	character specifying the type of threhsold to be returned: "static", "dynamic" or "both"
percentile	what percentile of the model should be use as a cut-off, e.g. 0.9, 0.95, or 0.99

Value

a list containing

Results	a `data.frame` with columns for the QC-ART scores, baseline indicators, time stamps and threshold values for each qc-art score
Static_Model	the 'lm' object that defines the final static model fit to the QC-ART scores
Dynamic_Model	the 'lm' object that defines the final static model fit to the QC-ART scores

Examples

#Compute the QC-ART scores.  For step-by-step instructions, see the documentation
#for the `qcart` function
library(lubridate)
library(QCART)
library(dplyr)
library(ggplot2)
data("amidan_et_al")  
amidan$Acq_Time_Start <- mdy_hm(amidan$Acq_Time_Start)
chosen_inst <- "VOrbiETD04"
vorb_04 <- filter(amidan,Instrument==chosen_inst)
vorb_04 <- arrange(vorb_04,Acq_Time_Start)
vorb_04 <- vorb_04[-c(1:6),]
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")
bline_ob <- 1:50
vorb_04$Baseline <- FALSE
vorb_04$Baseline[bline_ob] <- TRUE
vorb_04$QC_Art <- qcart(all_data = vorb_04, baseline = bline_ob, variables = chosen_vars)

#Compute a static threshold for the QC-ART scores.  Because there is no significant relationship between
#the QC-ART scores and time since the analysis began, the threshold value is the same for all time points.
s_threshold <- compute_threshold(scores = vorb_04$QC_Art, baseline = vorb_04$Baseline, time_stamps = vorb_04$Acq_Time_Start, type='static')
sthresh_df <- s_threshold$Results
qplot(Time_Stamp,Scores,data=sthresh_df,colour=Baseline)+xlab("Date")+ylab("QC-ART Score")+
  geom_line(aes(Time_Stamp,Static_Threshold),colour=1)
  
  
#Compute a dynamic threshold for the QC-ART scores.
d_threshold <- compute_threshold(scores = vorb_04$QC_Art, baseline = vorb_04$Baseline, time_stamps = vorb_04$Acq_Time_Start, type='dynamic')
dthresh_df <- d_threshold$Results
qplot(Time_Stamp,Scores,data=dthresh_df,colour=Baseline)+xlab("Date")+ylab("QC-ART Score")+
  geom_line(aes(Time_Stamp,Dynamic_Threshold),colour=1)

#Both dynamic and static thresholds can be computed in one call to `compute_threshold` by setting the 
#`type` argument to "both" 

both_thresholds <- compute_threshold(scores = vorb_04$QC_Art, baseline = vorb_04$Baseline, time_stamps = vorb_04$Acq_Time_Start, type='both')
all_thresh_df <- both_thresholds$Results
qplot(Time_Stamp,Scores,data=all_thresh_df,colour=Baseline)+xlab("Date")+ylab("QC-ART Score")+
  geom_line(aes(Time_Stamp,Static_Threshold),colour=1,linetype=1)+
  geom_line(aes(Time_Stamp,Dynamic_Threshold),colour=1,linetype=2)

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