highSCREEN (version 0.4)

hits: Identify hits

Description

description

Usage

hits(dat.raw, dat.norm, s0="S0", s1="S1", 
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 \(formatRESULT()\).

s0

Specifies the name of the columns containing t0-specific scores.

s1

Specifies the name of the columns containing t1-specific 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 t1-specific 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.

S0

Replicates of the score from the t0-specific data set.

S1

Replicates of the score from the t1-specific 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

# NOT RUN {
set.seed(1234)
nc = 24
nr = 16

# create 1st replicate of data matrix with compounds and controls
r1 = 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 replicate of data matrix with compounds and controls
r2 = matrix(abs(rnorm(nr*nc)*0.01), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
r3 = matrix(abs(rnorm(nr*nc)*0.01), nr, nc)

# combine all replicates for the t0-specific data
replicates_t0 = list(r1, r2, r3)
names(replicates_t0) = c("R1", "R2", "R3")

# create 1st replicate of data matrix with compounds and controls
r1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd replicate of data matrix with compounds and controls
r2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
r3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all replicates for the t1-specific data
replicates_t1 = list(r1, r2, r3)
names(replicates_t1) = c("R1", "R2", "R3")

# extract plate 1, replicate 1
dat1 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=1)

# extract plate 1, replicate 2
dat2 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=2)

# extract plate 1, replicate 3
dat3 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=3)

# no normalizion
datraw1 = normplate("Main Plate 1", dat1[["dat0"]], dat1[["dat1"]], cmap,
 plate=1, replicate=1, norm="raw")
datraw2 = normplate("Main Plate 1", dat2[["dat0"]], dat2[["dat1"]], cmap,
 plate=1, replicate=2, norm="raw")
datraw3 = normplate("Main Pltae 1", dat3[["dat0"]], dat3[["dat1"]], cmap,
 plate=1, replicate=3, norm="raw")

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

# reformat result
datraw = formatRESULT(datraw, replicate="Replicate", t="Time")

# c-score normalization
datnorm1 = normplate("Main Plate 1", dat1[["dat0"]], dat1[["dat1"]], cmap,
 plate=1, replicate=1, norm="cscore", 
poscont="Control P", negcont="Control N")
datnorm2 = normplate("Main Plate 1", dat2[["dat0"]], dat2[["dat1"]], cmap,
 plate=1, replicate=2, norm="cscore", 
poscont="Control P", negcont="Control N")
datnorm3 = normplate("Main Pltae 1", dat3[["dat0"]], dat3[["dat1"]], cmap,
 plate=1, replicate=3, norm="cscore",
poscont="Control P", negcont="Control N")

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

# reformat result
datnorm = formatRESULT(datnorm, replicate="Replicate", t="Time")

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