highSCREEN (version 0.1)

hits: title

Description

description

Usage

hits(dat.raw, dat.norm, score.before="scorebefore", score.after="scoreafter", 
qc.mainplates, qc1.val=0.225, hit.val=3)

Arguments

dat.raw

Data frame containing raw data as an output from $formatRESULT()$.

dat.norm

Data frame containing normalized data set as an output from $formatRESULT()$.

score.before

Specifies the name of the columns containing "Before" scores.

score.after

Specifies the name of the columns containing "After" scores.

qc.mainplates

A vector containing names of main plates that passed QC.

qc1.val

Threshold value for QC1.

hit.val

Threshold value for identifying candidate hits, based on the mean of "After" scores.

Value

The function returns a data frame. Each row corresponds to a compound that passed QC1 and belongs to a plate that passed overall QC. The data frame contains the following columns:

ID

Has the complete information to identify a compound or control. It contains information about the main plate, the quadrant/plate and the well.

MainPlate

Specifies the main plate to wich the compound/control belongs.

Plate

Specifies the quadrant/plate to wich the compound/control belongs.

Norm

Specifies the normalization method that was applied for the specific compound.

well

Specifies the location (row and column) of the compound/control in the quadrant.

row

Specifies the row location in the quadrant.

col

Specifies the column location in the quadrant.

welltype

Specifies if the well is compound or control.

scorebefore

Replicates of the score from the "Before" data set.

scoreafter

Replicates of the score from the "After" data set.

IND2

Indicator variable specifying if the compound passes ($TRUE$) or fails ($FALSE$) QC2.

IND3

Indicator variable specifying if the compound passes ($TRUE$) or fails ($FALSE$) QC3.

Examples

set.seed(1234)
nc = 24
nr = 16

# create 1st triplicate of data matrix with compounds and controls
replicate1 = matrix(abs(rnorm(nr*nc)*0.01), nr, nc)

# create control map
cmap = data.frame(X1=c(rep("Control P", floor(nr/3)), 
rep(c("Control low", "Control med", "Control high"), 
(floor(nr/3)+nr-3*floor(nr/3))/3), rep("Control N", 
floor(nr/3))), X2=c(rep("Control N", floor(nr/3)), 
rep(c("Control low", "Control med", "Control high"), 
(floor(nr/3)+nr-3*floor(nr/3))/3), rep("Control P", floor(nr/3))))
cmap = cmap[seq(1,nr,2),]

# create 2nd triplicate of data matrix with compounds and controls
replicate2 = matrix(abs(rnorm(nr*nc)*0.01), nr, nc)

# create 3rd triplicate of data matrix with compounds and controls
replicate3 = matrix(abs(rnorm(nr*nc)*0.01), nr, nc)

# combine all triplicates for the before data
replicates_before = list(replicate1, replicate2, replicate3)
names(replicates_before) = c("Replicate1", "Replicate2", "Replicate3")

# create 1st triplicate of data matrix with compounds and controls
replicate1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd triplicate of data matrix with compounds and controls
replicate2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd triplicate of data matrix with compounds and controls
replicate3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all triplicates for the after data
replicates_after = list(replicate1, replicate2, replicate3)
names(replicates_after) = c("Replicate1", "Replicate2", "Replicate3")

# extract plate 1, triplicate 1
dat1 = extractplate(replicates_before, replicates_after, plate=1, replicate=1)

# extract plate 1, triplicate 2
dat2 = extractplate(replicates_before, replicates_after, plate=1, replicate=2)

# extract plate 1, triplicate 3
dat3 = extractplate(replicates_before, replicates_after, plate=1, replicate=3)

# no normalizion
datraw1 = normplate("Main Plate 1", dat1[["datbefore"]], dat1[["datafter"]], cmap,
 plate=1, triplicate=1, norm="raw")
datraw2 = normplate("Main Plate 1", dat2[["datbefore"]], dat2[["datafter"]], cmap,
 plate=1, triplicate=2, norm="raw")
datraw3 = normplate("Main Pltae 1", dat3[["datbefore"]], dat3[["datafter"]], cmap,
 plate=1, triplicate=3, norm="raw")

# combine 3 triplicates
datraw = rbind(datraw1, datraw2, datraw3)

# reformat result
datraw = formatRESULT(datraw, triplicate="Triplicate", score="score", t="Time")

# c-score normalization
datnorm1 = normplate("Main Plate 1", dat1[["datbefore"]], dat1[["datafter"]], cmap,
 plate=1, triplicate=1, norm="cscore", 
poscont="Control P", negcont="Control N")
datnorm2 = normplate("Main Plate 1", dat2[["datbefore"]], dat2[["datafter"]], cmap,
 plate=1, triplicate=2, norm="cscore", 
poscont="Control P", negcont="Control N")
datnorm3 = normplate("Main Pltae 1", dat3[["datbefore"]], dat3[["datafter"]], cmap,
 plate=1, triplicate=3, norm="cscore",
poscont="Control P", negcont="Control N")

# combine 3 triplicates
datnorm = rbind(datnorm1, datnorm2, datnorm3)

# reformat result
datnorm = formatRESULT(datnorm, triplicate="Triplicate", score="score", t="Time")

# identify hits
head(hits(datraw, datnorm, qc.mainplates="Main Plate 1", qc1.val=0.225, hit.val=3))