zfactor.ssmd: Compute Z-factor and SSMD

Description Usage Arguments Value Examples

View source: R/zfactor.ssmd.R

Description

This function computes the Z-factor and strictly standardized mean difference (SSMD) of a given 96-well plate.

Usage

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zfactor.ssmd(dat, pos.cont, neg.cont, MainPlate, replicate)

Arguments

dat

Data frame as an output of the function formatRESULT().

pos.cont

Designation of positive control.

neg.cont

Designation of negative control.

MainPlate

Specifies main plate.

replicate

Specifies the replicate.

Value

Returns a data frame with one row and the following columns:

MainPlate

Specifies the main plate.

replicate

Specifies the replicate.

ZFactor_Before

Specifies the Z-factor computed based on the t0-specific data.

ZFactor_After

Specifies the Z-factor computed based on the t1-specific data.

SSMD_Before

Specifies SSMD computed based on the t0-specific data.

SSMD_After

Specifies SSMD computed based on the t1-specific data.

Examples

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

# create 1st replicate 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 replicate of data matrix with compounds and controls
replicate2 = matrix(abs(rnorm(nr*nc)), nr, nc)

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

# combine all replicates for the t0-specific data
replicates_before = list(replicate1, replicate2, replicate3)
names(replicates_before) = c("Replicate1", "Replicate2", "Replicate3")

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

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

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

# combine all replicates for the t1-specific data
replicates_after = list(replicate1, replicate2, replicate3)
names(replicates_after) = c("Replicate1", "Replicate2", "Replicate3")

# extract plate 1, replicate 1
dat1 = extractplate(replicates_before, replicates_after, plate=1, replicate=1)
# extract plate 1, replicate 2
dat2 = extractplate(replicates_before, replicates_after, plate=1, replicate=2)
# extract plate 1, replicate 3
dat3 = extractplate(replicates_before, replicates_after, 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 replicates
datraw = rbind(datraw1, datraw2, datraw3)

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

# compute z-factor and ssmd for each raw compound, replicate 1
zfactor.ssmd(datraw, "Control P", "Control N", "Main Plate 1", 1)

Example output

Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

[1] "raw"
[1] "raw"
[1] "raw"
     MainPlate replicate  ZFactor0  ZFactor1     SSMD0      SSMD1
1 Main Plate 1         1 -8.242231 -3.029124 0.3901324 -0.9424345

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