highSCREEN (version 0.1)

formatRESULT: title

Description

description

Usage

formatRESULT(dat, triplicate="Triplicate", score="score", t="Time")

Arguments

dat

Data frame such as the return data frame of the function $normplate()$.

triplicate

Specifies the column name of the input data frame that contains the triplicate numbers.

score

Specifies the column name of the input data frame that contains the normalized score values.

t

Specifies the column name of the input data frame that contains the time designations ("Before" and "After").

Value

This function returns a data frame with each row corresponding to a compound/control and 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.

Examples

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

# create 1st triplicate of data matrix with compounds and controls
replicate1 = matrix(abs(rnorm(nr*nc)), 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)), 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 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, all triplicates
dat1 = extractplate(replicates_before, replicates_after, plate=1, replicate=1)
dat2 = extractplate(replicates_before, replicates_after, plate=1, replicate=2)
dat3 = extractplate(replicates_before, replicates_after, plate=1, replicate=3)

# normalize data of all triplicates
res1 = normplate("Main Plate 1", dat1[["datbefore"]], dat1[["datafter"]], cmap, 
plate=1, triplicate=1, norm="zscore") 
res2 = normplate("Main Plate 1", dat2[["datbefore"]], dat2[["datafter"]], cmap, 
plate=1, triplicate=2, norm="zscore")
res3 = normplate("Main Plate 1", dat3[["datbefore"]], dat3[["datafter"]], cmap, 
plate=1, triplicate=3, norm="zscore")

# reformat data of all triplicates
head(formatRESULT(rbind(res1, res2, res3), triplicate="Triplicate", score="score", t="Time"))