Package 'LDAcoop' reference manual

Title:	Analysis of Data from Limiting Dilution Assay (LDA) with or without Cellular Cooperation
Description:	Cellular cooperation compromises the established method of calculating clonogenic activity from limiting dilution assay (LDA) data. This tool provides functions that enable robust analysis in presence or absence of cellular cooperation. The implemented method incorporates the same cooperativity module to model the non-linearity associated with cellular cooperation as known from the colony formation assay (Brix et al. (2021) <doi:10.1038/s41596-021-00615-0>: "Analysis of clonogenic growth in vitro." Nature protocols).
Authors:	Daniel Samaga [cre, aut], Nikko Brix [aut], Benedek Danko [aut], Kirsten Lauber [aut], Horst Zitzelsberger [aut]
Maintainer:	Daniel Samaga <[email protected]>
License:	GPL-3
Version:	0.1.2
Built:	2024-10-16 06:20:42 UTC
Source:	CRAN

LDA_activity

Description

calculation of clonogenic activities from data collected in a limiting dilution assay (LDA) experiment (i.e. cells, wells, positive wells, group).

Usage

LDA_activity(x, name = "LDA cells")
LDA_activity(x, name = "LDA cells")

Arguments

`x`	numeric data.frame or matrix with three columns (cells, wells, positive wells, group (optional))
`name`	optional: experiment name (e.g. name of cell line)

Value

list object with LDA-activities as returned by LDA_activity_single

Examples

x <- data.frame("cells" = c(10,50,100,250,10,50,100,250),
                "wells" = rep(25,8),
                "positive" = c(2,5,10,20,1,2,6,11),
                "group" = c(rep("A",4),rep("B",4)))
act <- LDA_activity(x)
x <- data.frame("cells" = c(10,50,100,250,10,50,100,250),
                "wells" = rep(25,8),
                "positive" = c(2,5,10,20,1,2,6,11),
                "group" = c(rep("A",4),rep("B",4)))
act <- LDA_activity(x)

LDA_activity_single

Description

calculation of clonogenic activity from data collected by a limiting dilution assay (LDA) experiment (i.e. numbers of: cells seeded, wells, positive wells).

Usage

LDA_activity_single(x, name = "cell line a", treat = "no")
LDA_activity_single(x, name = "cell line a", treat = "no")

Arguments

`x`	numeric data.frame or matrix with three columns (cells, wells, positive wells)
`name`	optional: experiment name (e.g. name of cell line)
`treat`	optional: treatment (e.g. irradiation dose in Gy)

Value

list object with estimated activity, 95 84 matrix, fit-object and p-value for cooperativity-test

Examples

x <- data.frame("cells" = c(10,50,100,250),
                "wells" = rep(25,4),
                "positive" = c(2,5,10,20))
act <- LDA_activity_single(x)
data(LDAdata)
cell.line <- unique(LDAdata$name)[1]
x <- subset.data.frame(
      LDAdata,
      subset = (name==cell.line) & (Group == 0))
LDA_activity_single(x[,4:6])
x <- data.frame("cells" = c(10,50,100,250),
                "wells" = rep(25,4),
                "positive" = c(2,5,10,20))
act <- LDA_activity_single(x)
data(LDAdata)
cell.line <- unique(LDAdata$name)[1]
x <- subset.data.frame(
      LDAdata,
      subset = (name==cell.line) & (Group == 0))
LDA_activity_single(x[,4:6])

LDA_plot

Description

plot clonogenic activity and survival (at more than one treatment group) for data from limiting dilution assay (LDA) experiments.

Usage

LDA_plot(LDA_tab, uncertainty = "act", xlim = NULL, uncertainty.band = FALSE)
LDA_plot(LDA_tab, uncertainty = "act", xlim = NULL, uncertainty.band = FALSE)

Arguments

`LDA_tab`	LDA data.frame ("cells", "wells", "positive", "group", "replicate")
`uncertainty`	method for uncertainty calculation ("act", "ep")
`xlim`	setting xlim of clonogenic activity plot
`uncertainty.band`	plotting of uncertainty bands TRUE/FALSE

Value

none

Examples

data(LDAdata)
Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
LDA_plot(Z1[,c("S-value","# Tested","# Clonal growth","Group","replicate")])
data(LDAdata)
Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
LDA_plot(Z1[,c("S-value","# Tested","# Clonal growth","Group","replicate")])

generate clonogenic activity estimation plot (frequency of negative wells over the number of cells seeded) for data of limiting dilution assay (LDA) experiments. Input is an data object as returned by the preprocessing function LDA_prepare_plot().

Usage

LDA_plot_activity(LDA_obj, xlim = NULL, uncertainty.band = FALSE)
LDA_plot_activity(LDA_obj, xlim = NULL, uncertainty.band = FALSE)

Arguments

`LDA_obj`	list returned from LDA_prepare_plot
`xlim`	manually setting the xlim
`uncertainty.band`	plotting uncertainty bands TRUE/FALSE

Value

none

Examples

x <- data.frame("cells" = rep(c(10,50,100,250),times = 4),
                "wells" = rep(25,16),
                "positive" = c(2,5,10,20,1,2,6,11,3,4,8,22,1,1,7,12),
                "group" = rep(c(rep("A",4),rep("B",4)),times = 2),
                "replicate" = c(rep(1,8),rep(2,8)))
out <- LDA_prepare_plot(x)
LDA_plot_activity(out[[1]])
data(LDAdata)
Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
out <- LDA_prepare_plot(Z1[,c("S-value","# Tested","# Clonal growth",
                              "Group","replicate")])
LDA_plot_activity(out[[1]])
x <- data.frame("cells" = rep(c(10,50,100,250),times = 4),
                "wells" = rep(25,16),
                "positive" = c(2,5,10,20,1,2,6,11,3,4,8,22,1,1,7,12),
                "group" = rep(c(rep("A",4),rep("B",4)),times = 2),
                "replicate" = c(rep(1,8),rep(2,8)))
out <- LDA_prepare_plot(x)
LDA_plot_activity(out[[1]])
data(LDAdata)
Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
out <- LDA_prepare_plot(Z1[,c("S-value","# Tested","# Clonal growth",
                              "Group","replicate")])
LDA_plot_activity(out[[1]])

LDA_plot_SF

Description

generate clonogenic survival plot (estimated clonogenic survival over treatment) for data from limiting dilution assay (LDA). Input is an data object as returned by the preprocessing function LDA_prepare_plot().

Usage

LDA_plot_SF(LDA_obj)
LDA_plot_SF(LDA_obj)

Arguments

LDA_obj

list returned from LDA_prepare_plot

Value

none

Examples

x <- data.frame("cells" = rep(c(10,50,100,250),times = 4),
                "wells" = rep(25,16),
                "positive" = c(2,5,10,20,1,2,6,11,3,4,8,22,1,1,7,12),
                "group" = rep(c(rep(0,4),rep(6,4)),times = 2),
                "replicate" = c(rep(1,8),rep(2,8)))
out <- LDA_prepare_plot(x)
LDA_plot_SF(out[[2]])
data(LDAdata)
Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
out <- LDA_prepare_plot(Z1[,c("S-value","# Tested","# Clonal growth",
                                "Group","replicate")])
LDA_plot_SF(out[[2]])
x <- data.frame("cells" = rep(c(10,50,100,250),times = 4),
                "wells" = rep(25,16),
                "positive" = c(2,5,10,20,1,2,6,11,3,4,8,22,1,1,7,12),
                "group" = rep(c(rep(0,4),rep(6,4)),times = 2),
                "replicate" = c(rep(1,8),rep(2,8)))
out <- LDA_prepare_plot(x)
LDA_plot_SF(out[[2]])
data(LDAdata)
Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
out <- LDA_prepare_plot(Z1[,c("S-value","# Tested","# Clonal growth",
                                "Group","replicate")])
LDA_plot_SF(out[[2]])

LDA_prepare_plot

Description

analyze limiting dilution assay (LDA) data and collect information for plotting.

Usage

LDA_prepare_plot(LDA_tab, uncertainty = "act")
LDA_prepare_plot(LDA_tab, uncertainty = "act")

Arguments

`LDA_tab`	LDA data.frame ("cells", "wells", "positive", "group", "replicate")
`uncertainty`	method for approximation of uncertainties of survival fractions (SF): activity based ("act") or by error propagation ("ep")

Value

none

Examples

x <- data.frame("cells" = rep(c(10,50,100,250),times = 4),
                "wells" = rep(25,16),
                "positive" = c(2,5,10,20,1,2,6,11,3,4,8,22,1,1,7,12),
                "group" = rep(c(rep("A",4),rep("B",4)),times = 2),
                "replicate" = c(rep(1,8),rep(2,8)))
LDA_prepare_plot(x)
# data(LDAdata)
# Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
# LDA_prepare_plot(Z1[,c("S-value","# Tested","# Clonal growth","Group",
#                      "replicate")])
x <- data.frame("cells" = rep(c(10,50,100,250),times = 4),
                "wells" = rep(25,16),
                "positive" = c(2,5,10,20,1,2,6,11,3,4,8,22,1,1,7,12),
                "group" = rep(c(rep("A",4),rep("B",4)),times = 2),
                "replicate" = c(rep(1,8),rep(2,8)))
LDA_prepare_plot(x)
# data(LDAdata)
# Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
# LDA_prepare_plot(Z1[,c("S-value","# Tested","# Clonal growth","Group",
#                      "replicate")])

LDA_survival

Description

calculation of clonogenic survival in a table of data from a limiting dilution assay (LDA) experiment (i.e. cells, wells, positive wells, group).

Usage

LDA_survival(x, name = "cell line a")
LDA_survival(x, name = "cell line a")

Arguments

`x`	numeric data.frame or matrix with three columns (cells, wells, positive wells, group)
`name`	optional: experiment name (e.g. name of cell line)

Value

list object with LDA-activities as returned by LDA_activity_single

Examples

x <- data.frame("cells" = c(10,50,100,250,10,50,100,250),
                "wells" = rep(25,8),
                "positive" = c(2,5,10,20,1,2,6,11),
                "group" = c(rep("A",4),rep("B",4)))
act <- LDA_survival(x)
x <- data.frame("cells" = c(10,50,100,250,10,50,100,250),
                "wells" = rep(25,8),
                "positive" = c(2,5,10,20,1,2,6,11),
                "group" = c(rep("A",4),rep("B",4)))
act <- LDA_survival(x)

LDA_survival_single

Description

calculate clonogenic survival fraction from LDA_activity objects.

Usage

LDA_survival_single(act.0, act.x)
LDA_survival_single(act.0, act.x)

Arguments

`act.0`	reference activity
`act.x`	activity after treatment

Value

list object with survival fraction, estimated confidence intervals (by error propagation through first order Taylor series approximation and by combination of 84

Examples

x.a <- data.frame("cells" = c(10,50,100,250),
                "wells" = rep(25,4),
                "positive" = c(2,5,10,20))
x.b <- data.frame("cells" = c(10,50,100,250),
                "wells" = rep(25,4),
                "positive" = c(1,2,6,11))
act.a <- LDA_activity_single(x.a)
act.b <- LDA_activity_single(x.b)
sf <- LDA_survival_single(act.0 = act.a,act.x = act.b)
data(LDAdata)
cell.line <- unique(LDAdata$name)[1]
x <- subset.data.frame(LDAdata, subset = (name==cell.line) & (Group < 2))
act <- LDA_activity(x[,c(4:6,3)])
sf <- LDA_survival_single(act.0 = act[[1]],act.x = act[[2]])
x.a <- data.frame("cells" = c(10,50,100,250),
                "wells" = rep(25,4),
                "positive" = c(2,5,10,20))
x.b <- data.frame("cells" = c(10,50,100,250),
                "wells" = rep(25,4),
                "positive" = c(1,2,6,11))
act.a <- LDA_activity_single(x.a)
act.b <- LDA_activity_single(x.b)
sf <- LDA_survival_single(act.0 = act.a,act.x = act.b)
data(LDAdata)
cell.line <- unique(LDAdata$name)[1]
x <- subset.data.frame(LDAdata, subset = (name==cell.line) & (Group < 2))
act <- LDA_activity(x[,c(4:6,3)])
sf <- LDA_survival_single(act.0 = act[[1]],act.x = act[[2]])

LDA_table

Description

show table with activities and clonogenic survival from limiting dilution assay (LDA) data.

Usage

LDA_table(x, ref_class = "unknown", uncertainty = "act")
LDA_table(x, ref_class = "unknown", uncertainty = "act")

Arguments

`x`	numeric data.frame or matrix with at least three columns (cells, wells, positive wells, group (optional))
`ref_class`	name of reference class for calculation of SF values
`uncertainty`	method for calculating the uncertainty bands of survival fractions ("act" (default) for combining the activity confidence intervals; "ep" for error propagation via first order Taylor series expansion.)

Value

table

Examples

x <- data.frame("cells" = c(10,50,100,250,10,50,100,250),
                "wells" = rep(25,8),
                "positive" = c(2,5,10,20,1,2,6,11),
                "group" = c(rep("A",4),rep("B",4)))
LDA_table(x,ref_class = "A")
x <- data.frame("cells" = c(10,50,100,250,10,50,100,250),
                "wells" = rep(25,8),
                "positive" = c(2,5,10,20,1,2,6,11),
                "group" = c(rep("A",4),rep("B",4)))
LDA_table(x,ref_class = "A")

LDA (limiting dilution assay) data from a set of cell lines

Description

LDA data from 11 cell lines, up to 4 biological replicates and up to 6 treatments.

Usage

data(LDAdata)
data(LDAdata)

Format

data.frame with columns: "name", "replicate", "Group", "S-value", "# Tested", "# Clonal growth"

Examples

data(LDAdata)
data(LDAdata)

Package 'LDAcoop'

Help Index

LDA_activity

Description

Usage

Arguments

Value

Examples

LDA_activity_single

Description

Usage

Arguments

Value

Examples

LDA_plot

Description

Usage

Arguments

Value

Examples

LDA_plot_activity

Description

Usage

Arguments

Value

Examples

LDA_plot_SF

Description

Usage

Arguments

Value

Examples

LDA_prepare_plot

Description

Usage

Arguments

Value

Examples

LDA_survival

Description

Usage

Arguments

Value

Examples

LDA_survival_single

Description

Usage

Arguments

Value

Examples

LDA_table

Description

Usage

Arguments

Value

Examples

LDA (limiting dilution assay) data from a set of cell lines

Description

Usage

Format

Examples