diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/drfit.R | 98 |
1 files changed, 63 insertions, 35 deletions
@@ -1,15 +1,25 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
- celltype="IPC-81",whereClause="1",
+ celltype="IPC-81",enzymetype="AChE",whereClause="1",
ok="'ok'")
{
library(RODBC)
- channel <- odbcConnect("cytotox",uid="cytotox",pwd="cytotox",case="tolower")
+ channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
slist <- paste(substances,collapse="','")
- query <- paste("SELECT conc,viability,unit,experimentator,substance,celltype,",
- "plate,ok FROM cytotox WHERE substance IN ('",
+ if (db == "cytotox") {
+ responsetype <- "viability"
+ testtype <- "celltype"
+ type <- celltype
+ } else {
+ responsetype <- "activity"
+ testtype <- "enzyme"
+ type <- enzymetype
+ }
+
+ query <- paste("SELECT conc,",responsetype,",unit,experimentator,substance,",testtype,
+ ",plate,ok FROM ", db, " WHERE substance IN ('",
slist,"') AND experimentator LIKE '",
- experimentator,"' AND celltype LIKE '",
- celltype,"' AND ",
+ experimentator,"' AND ",testtype," LIKE '",
+ type,"' AND ",
whereClause," AND ok in (",
ok,")",sep="")
data <- sqlQuery(channel,query)
@@ -36,7 +46,9 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, k*(1 + f*x) / (1 + ((2*f*(10^mu) + 1) * ((x/(10^mu))^b)))
}
- ri <- 0 # an index over the result rows
+ ri <- rix <- 0 # ri is the index over the result rows
+ # rix is used later to check if any
+ # model result was appended
rsubstance <- array() # the substance names in the results
rn <- vector() # number of dose-response curves
rlhd <- rlld <- vector() # highest and lowest doses tested
@@ -52,13 +64,13 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, for (i in substances) {
tmp <- splitted[[i]]
fit <- FALSE
+ n <- round(length(tmp$response)/9)
if (length(tmp$response) == 0) {
nodata = TRUE
} else {
nodata = FALSE
}
if (!nodata) {
- n <- round(length(tmp$response)/9)
if (is.na(startlogEC50[i])){
w <- 1/abs(tmp$response - 0.3)
startlogEC50[[i]] <- sum(w * log10(tmp$dose))/sum(w)
@@ -68,9 +80,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, lhd <- log10(highestdose)
lld <- log10(lowestdose)
responseathighestdose <- mean(subset(tmp,dose==highestdose)$response)
- rix <- ri # ri is the index of result lines
- # rix is used later to check if any
- # model result was appended
+ rix <- ri
if (responseathighestdose < 0.5) {
inactive <- FALSE
@@ -404,10 +414,19 @@ drplot <- function(drresults, data = FALSE, dtype = "std", alpha = 0.95, checkplate <- function(plate,db="cytotox")
{
library(RODBC)
- channel <- odbcConnect(db,uid=db,pwd=db,case="tolower")
+ channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+
+ if (db == "cytotox") {
+ responsetype <- "viability"
+ testtype <- "celltype"
+ } else {
+ responsetype <- "activity"
+ testtype <- "enzyme"
+ }
+
+ platequery <- paste("SELECT experimentator,substance,",testtype,",conc,unit,",responsetype,",performed,ok",
+ "FROM ",db," WHERE plate=", plate)
- platequery <- paste("SELECT experimentator,substance,celltype,conc,unit,viability,performed,ok FROM ",
- db," WHERE plate=", plate)
controlquery <- paste("SELECT type,response FROM controls WHERE plate=",plate)
platedata <- sqlQuery(channel,platequery)
@@ -419,7 +438,7 @@ checkplate <- function(plate,db="cytotox") cat("There is no response data for plate ",plate," in database ",db,"\n")
} else {
platedata$experimentator <- factor(platedata$experimentator)
- platedata$celltype <- factor(platedata$celltype)
+ platedata$type <- factor(platedata[[testtype]])
platedata$substance <- factor(platedata$substance)
platedata$unit <- factor(platedata$unit)
platedata$performed <- factor(platedata$performed)
@@ -437,7 +456,7 @@ checkplate <- function(plate,db="cytotox") cat("Plate ",plate," from database ",db,"\n",
"\tExperimentator: ",levels(platedata$experimentator),"\n",
- "\tCell type(s): ",levels(platedata$celltype),"\n",
+ "\tType(s): ",levels(platedata$type),"\n",
"\tPerformed on : ",levels(platedata$performed),"\n",
"\tSubstance(s): ",levels(platedata$substance),"\n",
"\tConcentration unit: ",levels(platedata$unit),"\n",
@@ -450,36 +469,46 @@ checkplate <- function(plate,db="cytotox") boxplot(blinds$response,controls$response,names=c("blinds","controls"),ylab="Response",main=paste("Plate ",plate))
- drdata <- subset(platedata,select=c(substance,conc,viability))
+ drdata <- platedata[c(2,4,6)]
drdata$substance <- factor(drdata$substance)
substances <- levels(drdata$substance)
- substances
plot(log10(drdata$conc),drdata$viability,
xlim=c(-2.5, 4.5),
ylim= c(-0.1, 2),
- xlab=paste("Decadic Logarithm of the concentration in ",levels(platedata$unit)),
- ylab="Viability")
+ xlab=paste("decadic logarithm of the concentration in ",levels(platedata$unit)),
+ ylab=responsetype)
drdatalist <- split(drdata,drdata$substance)
for (i in 1:length(drdatalist)) {
- points(log10(drdatalist[[i]]$conc),drdatalist[[i]]$viability,col=i);
+ points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsetype]],col=i);
}
legend(3.0,1.5,substances, pch=1, col=1:length(substances))
- title(main=paste("Plate ",plate," - ",levels(platedata$experimentator)," - ",levels(platedata$celltype)))
+ title(main=paste("Plate ",plate," - ",levels(platedata$experimentator)," - ",levels(platedata$type)))
}
}
-checksubstance <- function(substance,db="cytotox",experimentator="%",celltype="%",whereClause="1",ok="%")
+checksubstance <- function(substance,db="cytotox",experimentator="%",celltype="%",enzymetype="%",whereClause="1",ok="%")
{
library(RODBC)
- channel <- odbcConnect(db,uid=db,pwd=db,case="tolower")
- query <- paste("SELECT experimentator,substance,celltype,plate,conc,unit,viability,ok FROM cytotox WHERE substance LIKE '",
+ channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+
+ if (db == "cytotox") {
+ responsetype <- "viability"
+ testtype <- "celltype"
+ type <- celltype
+ } else {
+ responsetype <- "activity"
+ testtype <- "enzyme"
+ type <- enzymetype
+ }
+ query <- paste("SELECT experimentator,substance,",testtype,",plate,conc,unit,",responsetype,",ok",
+ " FROM ",db," WHERE substance LIKE '",
substance,"' AND experimentator LIKE '",
- experimentator,"' AND celltype LIKE '",
- celltype,"' AND ",
+ experimentator,"' AND ",testtype," LIKE '",
+ type,"' AND ",
whereClause," AND ok LIKE '",ok,"'",sep="")
data <- sqlQuery(channel,query)
@@ -488,7 +517,7 @@ checksubstance <- function(substance,db="cytotox",experimentator="%",celltype="% data$experimentator <- factor(data$experimentator)
data$substance <- factor(data$substance)
substances <- levels(data$substance)
- data$celltype <- factor(data$celltype)
+ data$type <- factor(data[[testtype]])
data$plate <- factor(data$plate)
plates <- levels(data$plate)
concentrations <- split(data$conc,data$conc)
@@ -500,25 +529,24 @@ checksubstance <- function(substance,db="cytotox",experimentator="%",celltype="% palette(rainbow(length(plates)))
}
- plot(log10(data$conc),data$viability,
+ plot(log10(data$conc),data[[responsetype]],
xlim=c(-2.5, 4.5),
ylim= c(-0.1, 2),
- xlab=paste("Decadic Logarithm of the concentration in ",levels(data$unit)),
- ylab="Viability")
+ xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)),
+ ylab=responsetype)
platelist <- split(data,data$plate)
for (i in 1:length(platelist)) {
- points(log10(platelist[[i]]$conc),platelist[[i]]$viability,col=i);
+ points(log10(platelist[[i]]$conc),platelist[[i]][[responsetype]],col=i);
}
legend(3.5,1.7,plates, pch=1, col=1:length(plates))
- title(main=paste(substance," - ",levels(data$experimentator)," - ",levels(data$celltype)))
+ title(main=paste(substance," - ",levels(data$experimentator)," - ",levels(data$type)))
cat("Substanz ",substance,"\n",
"\tExperimentator(s):",levels(data$experimentator),"\n",
- "\tCell type(s):\t",levels(data$celltype),"\n",
+ "\tType(s):\t",levels(data$type),"\n",
"\tSubstance(s):\t",levels(data$substance),"\n",
"\tPlate(s):\t",plates,"\n\n")
-
}
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