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R/qcQpcr.R
In qcQpcr: Histone ChIP-Seq qPCR Analyzer
#' A qPCR ChIP-seq QC function for Vii7 qPCR machine
#'
#' This function allows you to calculate qPCR Fold Enrichment
#' @author
#' Alireza Lorzadeh
#' @param x 'Vii7 result Excel sheet'
#' @param Name '.... Title for you graph, (ie: Projects name and date)'
#' @keywords qpcr
#' @examples
#' @import ggplot2
#'
#' Follow these steps to run the function:
#'
#' Install readxl package:
#' install.packages("readxl")
#'
#' Load the library:
#' library(readxl)
#'
#' Load the data:
#' <Data Name> <- read_excel("<path to file>",skip = 31)
#'
#' load ggplot:
#' library(ggplot2)
#'
#' Run the function:
#' qcQpcr(<Data Name>,'<.... Title for you graph>')
#'
#'
#'
#' Vii7 Data Set Example (Excel sheet):
#'
#' Block Type 384-Well Block
#' Calibration Background is expired Yes
#' Calibration Background performed on 2015-07-30 15:15:19 PM PDT
#' Calibration FAM is expired Yes
#' Calibration FAM performed on 2015-07-30 15:49:14 PM PDT
#' Calibration ROI is expired Yes
#' Calibration ROI performed on 2015-07-30 14:59:46 PM PDT
#' Calibration ROX is expired Yes
#' Calibration ROX performed on 2015-07-30 15:35:36 PM PDT
#' Calibration SYBR is expired Yes
#' Calibration SYBR performed on 2015-07-30 15:57:20 PM PDT
#' Calibration Uniformity is expired Yes
#' Calibration Uniformity performed on 2015-07-30 15:26:19 PM PDT
#' Calibration VIC is expired Yes
#' Calibration VIC performed on 2015-07-30 16:04:51 PM PDT
#' Chemistry SYBR_GREEN
#' Experiment Barcode
#' Experiment Comments
#' Experiment File Name
#' Experiment Name lINDAjAN22
#' Experiment Run End Time 2017-01-20 20:32:38 PM PST
#' Experiment Type Standard Curve
#' Experiment User Name
#' Instrument Name 278881968
#' Instrument Serial Number 278881968
#' Instrument Type ViiA 7
#' Passive Reference
#' Quantification Cycle Method Ct
#' Signal Smoothing On false
#' Stage/ Cycle where Analysis is performed Stage 2, Step 2
#'
#' Well Well Position Sample Name Target Name Task Reporter Quencher CT Ct Mean Ct SD
#' 1 A1 Ali_positive A1 H3K36me3 UNKNOWN SYBR None 25.193 24.972 0.313
#' 2 A2 Ali_positive A1 H3K36me3 UNKNOWN SYBR None 24.751 24.972 0.313
#' 3 A3 Ali_positive A2 H3K4me3 UNKNOWN SYBR None 25.697 25.710 0.019
#' 4 A4 Ali_positive A2 H3K4me3 UNKNOWN SYBR None 25.723 25.710 0.019
#' 5 A5 Ali_positive A3 H3K27me3 UNKNOWN SYBR None 27.441 28.853 1.997
#' 6 A6 Ali_positive A3 H3K27me3 UNKNOWN SYBR None 30.266 28.853 1.997
#' 7 A7 Ali_positive A4 H3K4me1 UNKNOWN SYBR None 24.839 24.810 0.041
#' 8 A8 Ali_positive A4 H3K4me1 UNKNOWN SYBR None 24.780 24.810 0.041
#' 9 A9 Ali_positive A5 H3K9me3 UNKNOWN SYBR None 22.599 22.613 0.020
#' 10 A10 Ali_positive A5 H3K9me3 UNKNOWN SYBR None 22.628 22.613 0.020
#' 14 A14 Ali_Input A-INPUT H3K36me3 UNKNOWN SYBR None 28.004 28.004
#' 15 A15 Ali_Input A-INPUT H3K36me3 UNKNOWN SYBR None Undetermined 28.004
#' 16 A16 Ali_Input A-INPUT H3K4me3 UNKNOWN SYBR None 31.282 29.791 2.107
#' 17 A17 Ali_Input A-INPUT H3K4me3 UNKNOWN SYBR None 28.301 29.791 2.107
#' 18 A18 Ali_Input A-INPUT H3K27me3 UNKNOWN SYBR None 24.940 26.424 2.099
#' 19 A19 Ali_Input A-INPUT H3K27me3 UNKNOWN SYBR None 27.908 26.424 2.099
#' 20 A20 Ali_Input A-INPUT H3K9me3 UNKNOWN SYBR None 27.509 26.876 0.895
#' 21 A21 Ali_Input A-INPUT H3K9me3 UNKNOWN SYBR None 26.243 26.876 0.895
#' 25 B1 Ali_Negative A1 H3K36me3 UNKNOWN SYBR None 28.515 28.158 0.505
#' 26 B2 Ali_Negative A1 H3K36me3 UNKNOWN SYBR None 27.801 28.158 0.505
#' 27 B3 Ali_Negative A2 H3K4me3 UNKNOWN SYBR None 17.982 17.983 0.001
#' 28 B4 Ali_Negative A2 H3K4me3 UNKNOWN SYBR None 17.984 17.983 0.001
#' 29 B5 Ali_Negative A3 H3K27me3 UNKNOWN SYBR None 26.677 26.708 0.043
#' 30 B6 Ali_Negative A3 H3K27me3 UNKNOWN SYBR None 26.738 26.708 0.043
#' 31 B7 Ali_Negative A4 H3K4me1 UNKNOWN SYBR None 23.196 23.159 0.052
#' 32 B8 Ali_Negative A4 H3K4me1 UNKNOWN SYBR None 23.123 23.159 0.052
#' 33 B9 Ali_Negative A5 H3K9me3 UNKNOWN SYBR None 25.911 26.133 0.315
#' 34 B10 Ali_Negative A5 H3K9me3 UNKNOWN SYBR None 26.356 26.133 0.315
#' 38 B14 NTC H3K36me3 NTC SYBR None Undetermined
#' 39 B15 NTC H3K36me3 NTC SYBR None Undetermined
#' 40 B16 NTC H3K4me3 NTC SYBR None Undetermined
#' 41 B17 NTC H3K4me3 NTC SYBR None Undetermined
#' 42 B18 NTC H3K27me3 NTC SYBR None Undetermined
#' 43 B19 NTC H3K27me3 NTC SYBR None Undetermined
#' 44 B20 NTC H3K9me3 NTC SYBR None Undetermined
#' 45 B21 NTC H3K9me3 NTC SYBR None Undetermined
#' 49 C1 Sample2_positive B1 H3K36me3 UNKNOWN SYBR None 24.426 24.343 0.117
#' 50 C2 Sample2_positive B1 H3K36me3 UNKNOWN SYBR None 24.260 24.343 0.117
#' 51 C3 Sample2_positive B2 H3K4me3 UNKNOWN SYBR None 25.490 25.470 0.029
#' 52 C4 Sample2_positive B2 H3K4me3 UNKNOWN SYBR None 25.450 25.470 0.029
#' 53 C5 Sample2_positive B3 H3K27me3 UNKNOWN SYBR None 26.351 26.312 0.055
#' 54 C6 Sample2_positive B3 H3K27me3 UNKNOWN SYBR None 26.273 26.312 0.055
#' 55 C7 Sample2_positive B4 H3K4me1 UNKNOWN SYBR None 24.452 24.307 0.205
#' 56 C8 Sample2_positive B4 H3K4me1 UNKNOWN SYBR None 24.162 24.307 0.205
#' 57 C9 Sample2_positive B5 H3K9me3 UNKNOWN SYBR None 23.149 23.144 0.007
#' 58 C10 Sample2_positive B5 H3K9me3 UNKNOWN SYBR None 23.139 23.144 0.007
#' 62 C14 Sample2_Input B-INPUT H3K36me3 UNKNOWN SYBR None 28.284 28.106 0.252
#' 63 C15 Sample2_Input B-INPUT H3K36me3 UNKNOWN SYBR None 27.928 28.106 0.252
#' 64 C16 Sample2_Input B-INPUT H3K4me3 UNKNOWN SYBR None 32.615 32.400 0.303
#' 65 C17 Sample2_Input B-INPUT H3K4me3 UNKNOWN SYBR None 32.186 32.400 0.303
#' 66 C18 Sample2_Input B-INPUT H3K27me3 UNKNOWN SYBR None 25.584 25.743 0.225
#' 67 C19 Sample2_Input B-INPUT H3K27me3 UNKNOWN SYBR None 25.902 25.743 0.225
#' 68 C20 Sample2_Input B-INPUT H3K9me3 UNKNOWN SYBR None 28.429 28.414 0.021
#' 69 C21 Sample2_Input B-INPUT H3K9me3 UNKNOWN SYBR None 28.399 28.414 0.021
#' 73 D1 Sample2_Negative B1 H3K36me3 UNKNOWN SYBR None 28.756 28.662 0.132
#' 74 D2 Sample2_Negative B1 H3K36me3 UNKNOWN SYBR None 28.569 28.662 0.132
#' 75 D3 Sample2_Negative B2 H3K4me3 UNKNOWN SYBR None 17.547 17.538 0.012
#' 76 D4 Sample2_Negative B2 H3K4me3 UNKNOWN SYBR None 17.530 17.538 0.012
#' 77 D5 Sample2_Negative B3 H3K27me3 UNKNOWN SYBR None 26.061 26.074 0.019
#' 78 D6 Sample2_Negative B3 H3K27me3 UNKNOWN SYBR None 26.088 26.074 0.019
#' 79 D7 Sample2_Negative B4 H3K4me1 UNKNOWN SYBR None 22.784 22.796 0.017
#' 80 D8 Sample2_Negative B4 H3K4me1 UNKNOWN SYBR None 22.808 22.796 0.017
#' 81 D9 Sample2_Negative B5 H3K9me3 UNKNOWN SYBR None 26.750 26.798 0.068
#' 82 D10 Sample2_Negative B5 H3K9me3 UNKNOWN SYBR None 26.847 26.798 0.068
NULL
library(ggplot2)
globalVariables(c("Sample", "FoldEn","Target"))
qcQpcr <- function(xx,Name) {
Data<-data.frame(Sample = character(),
Mark = character(),
Target = character(),
FoldEn = numeric(0))
x<-xx[-(grep('NTC',xx$`Sample Name`)),]
b<-unique(x$`Sample Name`)
b<-b[!(is.na(b))]
c<-b
c<-sub("*_.*","",c)
c<-c(unique(c))
bb<-x[grep("positive",x$`Sample Name`),]
d<-unique(bb$`Target Name`)
d<-d[!(is.na(d))]
i <- 1
for (i in i:length(d)){
ii <- 1
for (ii in ii:length(c)){
if(d[i] == "H3K4me1"){
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
mark<- x[grep('H3K36me3',x$`Target Name`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K4me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K27me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K9me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K27me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K27me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K36me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K36me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
mark<- x[grep('H3K4me3',x$`Target Name`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
Data<-rbind(Data,data)
}
}
x <- y <- NULL
ggplot(Data,aes(x=Sample,y=FoldEn,fill=Target))+
geom_bar(stat="identity",position=position_dodge())+
scale_fill_manual(values=c("red","blue"))+
facet_wrap(~Mark,scales="free")+
ggtitle(Name)
}
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#' A qPCR ChIP-seq QC function for Vii7 qPCR machine
#'
#' This function allows you to calculate qPCR Fold Enrichment
#' @author
#' Alireza Lorzadeh
#' @param x 'Vii7 result Excel sheet'
#' @param Name '.... Title for you graph, (ie: Projects name and date)'
#' @keywords qpcr
#' @examples
#' @import ggplot2
#'
#' Follow these steps to run the function:
#'
#' Install readxl package:
#' install.packages("readxl")
#'
#' Load the library:
#' library(readxl)
#'
#' Load the data:
#' <Data Name> <- read_excel("<path to file>",skip = 31)
#'
#' load ggplot:
#' library(ggplot2)
#'
#' Run the function:
#' qcQpcr(<Data Name>,'<.... Title for you graph>')
#'
#'
#'
#' Vii7 Data Set Example (Excel sheet):
#'
#' Block Type 384-Well Block
#' Calibration Background is expired Yes
#' Calibration Background performed on 2015-07-30 15:15:19 PM PDT
#' Calibration FAM is expired Yes
#' Calibration FAM performed on 2015-07-30 15:49:14 PM PDT
#' Calibration ROI is expired Yes
#' Calibration ROI performed on 2015-07-30 14:59:46 PM PDT
#' Calibration ROX is expired Yes
#' Calibration ROX performed on 2015-07-30 15:35:36 PM PDT
#' Calibration SYBR is expired Yes
#' Calibration SYBR performed on 2015-07-30 15:57:20 PM PDT
#' Calibration Uniformity is expired Yes
#' Calibration Uniformity performed on 2015-07-30 15:26:19 PM PDT
#' Calibration VIC is expired Yes
#' Calibration VIC performed on 2015-07-30 16:04:51 PM PDT
#' Chemistry SYBR_GREEN
#' Experiment Barcode
#' Experiment Comments
#' Experiment File Name
#' Experiment Name lINDAjAN22
#' Experiment Run End Time 2017-01-20 20:32:38 PM PST
#' Experiment Type Standard Curve
#' Experiment User Name
#' Instrument Name 278881968
#' Instrument Serial Number 278881968
#' Instrument Type ViiA 7
#' Passive Reference
#' Quantification Cycle Method Ct
#' Signal Smoothing On false
#' Stage/ Cycle where Analysis is performed Stage 2, Step 2
#'
#' Well Well Position Sample Name Target Name Task Reporter Quencher CT Ct Mean Ct SD
#' 1 A1 Ali_positive A1 H3K36me3 UNKNOWN SYBR None 25.193 24.972 0.313
#' 2 A2 Ali_positive A1 H3K36me3 UNKNOWN SYBR None 24.751 24.972 0.313
#' 3 A3 Ali_positive A2 H3K4me3 UNKNOWN SYBR None 25.697 25.710 0.019
#' 4 A4 Ali_positive A2 H3K4me3 UNKNOWN SYBR None 25.723 25.710 0.019
#' 5 A5 Ali_positive A3 H3K27me3 UNKNOWN SYBR None 27.441 28.853 1.997
#' 6 A6 Ali_positive A3 H3K27me3 UNKNOWN SYBR None 30.266 28.853 1.997
#' 7 A7 Ali_positive A4 H3K4me1 UNKNOWN SYBR None 24.839 24.810 0.041
#' 8 A8 Ali_positive A4 H3K4me1 UNKNOWN SYBR None 24.780 24.810 0.041
#' 9 A9 Ali_positive A5 H3K9me3 UNKNOWN SYBR None 22.599 22.613 0.020
#' 10 A10 Ali_positive A5 H3K9me3 UNKNOWN SYBR None 22.628 22.613 0.020
#' 14 A14 Ali_Input A-INPUT H3K36me3 UNKNOWN SYBR None 28.004 28.004
#' 15 A15 Ali_Input A-INPUT H3K36me3 UNKNOWN SYBR None Undetermined 28.004
#' 16 A16 Ali_Input A-INPUT H3K4me3 UNKNOWN SYBR None 31.282 29.791 2.107
#' 17 A17 Ali_Input A-INPUT H3K4me3 UNKNOWN SYBR None 28.301 29.791 2.107
#' 18 A18 Ali_Input A-INPUT H3K27me3 UNKNOWN SYBR None 24.940 26.424 2.099
#' 19 A19 Ali_Input A-INPUT H3K27me3 UNKNOWN SYBR None 27.908 26.424 2.099
#' 20 A20 Ali_Input A-INPUT H3K9me3 UNKNOWN SYBR None 27.509 26.876 0.895
#' 21 A21 Ali_Input A-INPUT H3K9me3 UNKNOWN SYBR None 26.243 26.876 0.895
#' 25 B1 Ali_Negative A1 H3K36me3 UNKNOWN SYBR None 28.515 28.158 0.505
#' 26 B2 Ali_Negative A1 H3K36me3 UNKNOWN SYBR None 27.801 28.158 0.505
#' 27 B3 Ali_Negative A2 H3K4me3 UNKNOWN SYBR None 17.982 17.983 0.001
#' 28 B4 Ali_Negative A2 H3K4me3 UNKNOWN SYBR None 17.984 17.983 0.001
#' 29 B5 Ali_Negative A3 H3K27me3 UNKNOWN SYBR None 26.677 26.708 0.043
#' 30 B6 Ali_Negative A3 H3K27me3 UNKNOWN SYBR None 26.738 26.708 0.043
#' 31 B7 Ali_Negative A4 H3K4me1 UNKNOWN SYBR None 23.196 23.159 0.052
#' 32 B8 Ali_Negative A4 H3K4me1 UNKNOWN SYBR None 23.123 23.159 0.052
#' 33 B9 Ali_Negative A5 H3K9me3 UNKNOWN SYBR None 25.911 26.133 0.315
#' 34 B10 Ali_Negative A5 H3K9me3 UNKNOWN SYBR None 26.356 26.133 0.315
#' 38 B14 NTC H3K36me3 NTC SYBR None Undetermined
#' 39 B15 NTC H3K36me3 NTC SYBR None Undetermined
#' 40 B16 NTC H3K4me3 NTC SYBR None Undetermined
#' 41 B17 NTC H3K4me3 NTC SYBR None Undetermined
#' 42 B18 NTC H3K27me3 NTC SYBR None Undetermined
#' 43 B19 NTC H3K27me3 NTC SYBR None Undetermined
#' 44 B20 NTC H3K9me3 NTC SYBR None Undetermined
#' 45 B21 NTC H3K9me3 NTC SYBR None Undetermined
#' 49 C1 Sample2_positive B1 H3K36me3 UNKNOWN SYBR None 24.426 24.343 0.117
#' 50 C2 Sample2_positive B1 H3K36me3 UNKNOWN SYBR None 24.260 24.343 0.117
#' 51 C3 Sample2_positive B2 H3K4me3 UNKNOWN SYBR None 25.490 25.470 0.029
#' 52 C4 Sample2_positive B2 H3K4me3 UNKNOWN SYBR None 25.450 25.470 0.029
#' 53 C5 Sample2_positive B3 H3K27me3 UNKNOWN SYBR None 26.351 26.312 0.055
#' 54 C6 Sample2_positive B3 H3K27me3 UNKNOWN SYBR None 26.273 26.312 0.055
#' 55 C7 Sample2_positive B4 H3K4me1 UNKNOWN SYBR None 24.452 24.307 0.205
#' 56 C8 Sample2_positive B4 H3K4me1 UNKNOWN SYBR None 24.162 24.307 0.205
#' 57 C9 Sample2_positive B5 H3K9me3 UNKNOWN SYBR None 23.149 23.144 0.007
#' 58 C10 Sample2_positive B5 H3K9me3 UNKNOWN SYBR None 23.139 23.144 0.007
#' 62 C14 Sample2_Input B-INPUT H3K36me3 UNKNOWN SYBR None 28.284 28.106 0.252
#' 63 C15 Sample2_Input B-INPUT H3K36me3 UNKNOWN SYBR None 27.928 28.106 0.252
#' 64 C16 Sample2_Input B-INPUT H3K4me3 UNKNOWN SYBR None 32.615 32.400 0.303
#' 65 C17 Sample2_Input B-INPUT H3K4me3 UNKNOWN SYBR None 32.186 32.400 0.303
#' 66 C18 Sample2_Input B-INPUT H3K27me3 UNKNOWN SYBR None 25.584 25.743 0.225
#' 67 C19 Sample2_Input B-INPUT H3K27me3 UNKNOWN SYBR None 25.902 25.743 0.225
#' 68 C20 Sample2_Input B-INPUT H3K9me3 UNKNOWN SYBR None 28.429 28.414 0.021
#' 69 C21 Sample2_Input B-INPUT H3K9me3 UNKNOWN SYBR None 28.399 28.414 0.021
#' 73 D1 Sample2_Negative B1 H3K36me3 UNKNOWN SYBR None 28.756 28.662 0.132
#' 74 D2 Sample2_Negative B1 H3K36me3 UNKNOWN SYBR None 28.569 28.662 0.132
#' 75 D3 Sample2_Negative B2 H3K4me3 UNKNOWN SYBR None 17.547 17.538 0.012
#' 76 D4 Sample2_Negative B2 H3K4me3 UNKNOWN SYBR None 17.530 17.538 0.012
#' 77 D5 Sample2_Negative B3 H3K27me3 UNKNOWN SYBR None 26.061 26.074 0.019
#' 78 D6 Sample2_Negative B3 H3K27me3 UNKNOWN SYBR None 26.088 26.074 0.019
#' 79 D7 Sample2_Negative B4 H3K4me1 UNKNOWN SYBR None 22.784 22.796 0.017
#' 80 D8 Sample2_Negative B4 H3K4me1 UNKNOWN SYBR None 22.808 22.796 0.017
#' 81 D9 Sample2_Negative B5 H3K9me3 UNKNOWN SYBR None 26.750 26.798 0.068
#' 82 D10 Sample2_Negative B5 H3K9me3 UNKNOWN SYBR None 26.847 26.798 0.068
NULL
library(ggplot2)
globalVariables(c("Sample", "FoldEn","Target"))
qcQpcr <- function(xx,Name) {
Data<-data.frame(Sample = character(),
Mark = character(),
Target = character(),
FoldEn = numeric(0))
x<-xx[-(grep('NTC',xx$`Sample Name`)),]
b<-unique(x$`Sample Name`)
b<-b[!(is.na(b))]
c<-b
c<-sub("*_.*","",c)
c<-c(unique(c))
bb<-x[grep("positive",x$`Sample Name`),]
d<-unique(bb$`Target Name`)
d<-d[!(is.na(d))]
i <- 1
for (i in i:length(d)){
ii <- 1
for (ii in ii:length(c)){
if(d[i] == "H3K4me1"){
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
mark<- x[grep('H3K36me3',x$`Target Name`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K4me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K27me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K9me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K27me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K27me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K36me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
if(d[i] == "H3K36me3") {
temp<-c[ii]
mark<- x[grep(d[i],x$`Target Name`),]
pos<-mark[grep(paste(c[ii], "positive", sep="_"),mark$`Sample Name`),]
pos<- pos[!duplicated( pos$`Ct Mean`),]
neg<-mark[grep(paste(c[ii], "Negative", sep="_"),mark$`Sample Name`),]
neg<- neg[!duplicated( neg$`Ct Mean`),]
mark<- x[grep('H3K4me3',x$`Target Name`),]
inp<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp<- inp[!duplicated( inp$`Ct Mean`),]
mark<- x[grep('H3K9me3',x$`Target Name`),]
inp_neg<-mark[grep(paste(c[ii], "Input", sep="_"),mark$`Sample Name`),]
inp_neg<- inp[!duplicated( inp$`Ct Mean`),]
p<-2^(inp$`Ct Mean` - pos$`Ct Mean`)
n<-2^(inp_neg$`Ct Mean` - neg$`Ct Mean`)
data<-data.frame(Sample = c(temp,temp),
Mark = c(d[i],d[i]),
Target = c('Positive',"Negative"),
FoldEn = c(p,n))
}
Data<-rbind(Data,data)
}
}
x <- y <- NULL
ggplot(Data,aes(x=Sample,y=FoldEn,fill=Target))+
geom_bar(stat="identity",position=position_dodge())+
scale_fill_manual(values=c("red","blue"))+
facet_wrap(~Mark,scales="free")+
ggtitle(Name)
}
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