formatRESULT: Format results

In highSCREEN: High-Throughput Screening for Plate Based Essays

Description

description

Usage

formatRESULT(dat, replicate="Replicate", score="S", t="Time")

Arguments

dat	Data frame such as the return data frame of the function normplate().
replicate	Specifies the column name of the input data frame that contains the replicate 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 (0 or 1).

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.
S0	Replicates of the score from the t0-specific data set.
S1	Replicates of the score from the t1-specific data set.

Examples

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

# create 1st replicate of data matrix with compounds and controls
r1 = 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 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 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, all replicates
dat1 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=1)
dat2 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=2)
dat3 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=3)

# normalize data of all replicates
res1 = normplate("Main Plate 1", dat1[["dat0"]], dat1[["dat1"]], cmap, 
plate=1, replicate=1, norm="zscore") 
res2 = normplate("Main Plate 1", dat2[["dat0"]], dat2[["dat1"]], cmap, 
plate=1, replicate=2, norm="zscore")
res3 = normplate("Main Plate 1", dat3[["dat0"]], dat3[["dat1"]], cmap, 
plate=1, replicate=3, norm="zscore")

# reformat data of all replicates
head(formatRESULT(rbind(res1, res2, res3), replicate="Replicate", t="Time"))

highSCREEN documentation built on Feb. 12, 2021, 5:09 p.m.