Description Usage Arguments Details Value Note Author(s) References Examples
View source: R/Z3_estimate_normalization_factor_House_keeping_genes.r
Estimate normalization factor using house-keeping genes
1 | BridgeRNormalizationFactorsHK(InputFile, group, hour, InforColumn = 4, InforHKGenes = 2, HKGenes = c("GAPDH", "PGK1", "PPIA", "ENO1", "ATP5B", "ALDOA"), OutputFile = "BridgeR_3B_Normalizaion_factor_from_House_keeping_genes.txt")
|
InputFile |
File path/name |
group |
Vector(string) |
hour |
Vector(number) |
InforColumn |
Integer |
InforHKGenes |
Integer |
HKGenes |
Vector(String) |
OutputFile |
File path/name |
Estimate normalization factor using house-keeping genes
text file
2015-11-05
Naoto Imamachi
https://github.com/Naoto-Imamachi/BRIC-seq_data_analysis/tree/master/BridgeR
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
#inputfile <- "BridgeR_1_Relative_expression_dataset.txt"
#outputfile <- "BridgeR_3_Normalizaion_factor_HouseKeepingGenes.txt"
#group <- c("Control","knockdown1","knockdown2")
#hour <- c(0,1,2,4,8,12)
#BridgeRNormalizationFactorsHK(InputFile=inputfile, group=group, hour=hour, OutputFile=outputfile)
## The function is currently defined as
function (InputFile, group, hour, InforColumn = 4, InforHKGenes = 2,
HKGenes = c("GAPDH", "PGK1", "PPIA", "ENO1", "ATP5B", "ALDOA"),
OutputFile = "BridgeR_3B_Normalizaion_factor_from_House_keeping_genes.txt")
{
group_number <- length(group)
time_points <- length(hour)
input_file <- fread(InputFile, header = T)
hour_label <- NULL
for (x in hour) {
label <- x
if (x < 10) {
label <- paste("0", x, sep = "")
}
hour_label <- append(hour_label, paste("T", label, "_",
a, sep = ""))
}
cat("Sample", hour_label, sep = "\t", file = OutputFile)
cat("\n", file = OutputFile, append = T)
for (a in 1:group_number) {
HKgenes_infor <- input_file[[InforHKGenes]]
HKgenes_infor_index <- NULL
for (x in 1:length(HKGenes)) {
HKgenes_infor_index <- append(HKgenes_infor_index,
which(HKgenes_infor == HKGenes[x]))
}
infor_st <- 1 + (a - 1) * (time_points + InforColumn)
infor_ed <- (InforColumn) * a + (a - 1) * time_points
exp_st <- infor_ed + 1
exp_ed <- infor_ed + time_points
HKGenes_raw_data <- NULL
for (x in 1:length(HKgenes_infor_index)) {
if (x == 1) {
HKGenes_raw_data <- input_file[HKgenes_infor_index[x],
exp_st:exp_ed, with = F]
}
else {
HKGenes_raw_data <- rbind(HKGenes_raw_data, input_file[HKgenes_infor_index[x],
exp_st:exp_ed, with = F])
}
}
nf <- NULL
for (x in 1:length(HKGenes_raw_data)) {
if (x == 1) {
nf <- as.vector(as.matrix(HKGenes_raw_data[x,
]))
}
else {
nf <- HKGenes_raw_data[x, ] * nf
}
}
nf <- nf^(1/length(HKGenes))
cat(group[a], nf, sep = "\t", file = OutputFile, append = T)
cat("\n", file = OutputFile, append = T)
}
}
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