R/getWorklist.R
In jaspershen/sxtTools: All the usefull tools from Xiaotao Shen
#' @title getWorklist
#' @description Generate Worklist for MS data acquisition.
#' @author Xiaotao Shen
#' \email{shenxt@@sioc.ac.cn}
#' @param instrument Which instrument you use?
#' "Agilent", "AB" or "Thermo", default is "Thermo".
#' @param name The name of worklist.
#' @param randommethod Which random method you want to use?
#' "no", "position" or "injection". Default is "no".
#' @param samplenumber Sample number.
#' @param replication Replication times.
#' @param QCstep QC step.
#' @param conditionQCnumber Condition QC number.
#' @param validationQCstep Validation QC step.
#' @param testmixstep Test mixture step.
#' @param injectionfrom Injection order from which? Default is 1.
#' @param user Default is "other".
#' @param dir Directory.
#' @return New worklist.
#' @export
setGeneric(
name = "getWorklist",
def = function(table.name = "batch1.xlsx",
instrument = c("Thermo", "Agilent", "AB"),
each.mode.number = 30,
randommethod = c("no", "position", "injection"),
samplenumber = NULL,
replication = 1,
QCstep = 8,
conditionQCnumber = 5,
qc.index.from = 1,
dir = "D:\\Liang\\SmarD_Urine_20190731\\RPLC\\",
method.path = "D:\\Liang\\Methods\\RPLC\\Urine\\",
ms1.method.pos = "Hypersil_GOLD_MS_pos",
ms1.method.neg = "Hypersil_GOLD_MS_neg",
ms2.method.pos = c("Hypersil_GOLD_MSMS_pos_NCE25_70_250",
"Hypersil_GOLD_MSMS_pos_NCE25_240_400",
"Hypersil_GOLD_MSMS_pos_NCE25_390_600",
"Hypersil_GOLD_MSMS_pos_NCE25_590_1000",
"Hypersil_GOLD_MSMS_pos_NCE50_70_250",
"Hypersil_GOLD_MSMS_pos_NCE50_240_400",
"Hypersil_GOLD_MSMS_pos_NCE50_390_600",
"Hypersil_GOLD_MSMS_pos_NCE50_590_1000"),
ms2.method.neg = c("Hypersil_GOLD_MSMS_neg_NCE25_70_250",
"Hypersil_GOLD_MSMS_neg_NCE25_240_400",
"Hypersil_GOLD_MSMS_neg_NCE25_390_600",
"Hypersil_GOLD_MSMS_neg_NCE25_590_1000",
"Hypersil_GOLD_MSMS_neg_NCE50_70_250",
"Hypersil_GOLD_MSMS_neg_NCE50_240_400",
"Hypersil_GOLD_MSMS_neg_NCE50_390_600",
"Hypersil_GOLD_MSMS_neg_NCE50_590_1000")
) {
instrument <- match.arg(instrument)
randommethod <- match.arg(randommethod)
options(warn = -1)
file <- dir()
if (instrument == "Thermo") {
batch <- readxl::read_excel(table.name)
if (randommethod == "no") {
###add position
position <-
unlist(lapply(c("B", "G", "R"), function(y) {
paste(y,
unlist(lapply(LETTERS[1:5], function(x) {
paste(x, 1:8, sep = "")
})),
sep = "")
}))
position <- position[-c(1:8)]
condition.qc <-
matrix(rep(
c("Condition.QC", 'Condition.QC', "BA1"),
conditionQCnumber
),
ncol = 3,
byrow = TRUE)
condition.qc <-
as.data.frame(condition.qc, stringsAsFactors = FALSE)
colnames(condition.qc) <-
c("File.Name", "Sample.ID", 'Position')
blank.qc <-
data.frame(
"File.Name" = c("Blank", "QC"),
"Sample.ID" = c("Blank", "QC"),
"Position" = c("BA2", "BA1"),
stringsAsFactors = FALSE
)
blank <-
data.frame(
"File.Name" = c("Blank", "Blank", "Blank"),
"Sample.ID" = c("Blank", "Blank", "Blank"),
"Position" = c("BA2", "BA2", "BA2"),
stringsAsFactors = FALSE
)
dilution.qc <- data.frame(
"File.Name" = c("DL_QC1_1", "DL_QC2_1", "DL_QC4_1", "DL_QC8_1", "DL_QC1_2", "DL_QC2_2", "DL_QC4_2", "DL_QC8_2"),
"Sample.ID" = c("DL_QC1_1", "DL_QC2_1", "DL_QC4_1", "DL_QC8_1", "DL_QC1_2", "DL_QC2_2", "DL_QC4_2", "DL_QC8_2"),
"Position" = c("BA3", "BA4", "BA5", "BA6", "BA3", "BA4", "BA5", "BA6"),
stringsAsFactors = FALSE
)
ms2.qc <-
data.frame(
"File.Name" = c("QC_MS2_NCE25_1", "QC_MS2_NCE25_2", "QC_MS2_NCE25_3", "QC_MS2_NCE25_4",
"QC_MS2_NCE50_1", "QC_MS2_NCE50_2", "QC_MS2_NCE50_3", "QC_MS2_NCE50_4"),
"Sample.ID" = c("QC_MS2_NCE25_1", "QC_MS2_NCE25_2", "QC_MS2_NCE25_3", "QC_MS2_NCE25_4",
"QC_MS2_NCE50_1", "QC_MS2_NCE50_2", "QC_MS2_NCE50_3", "QC_MS2_NCE50_4"),
"Position" = c("BA1", "BA1", "BA1", "BA1", "BA1", "BA1", "BA1", "BA1"),
stringsAsFactors = FALSE
)
batch <- cbind(batch, batch)
batch <- data.frame(batch,
"Position" = rep(position, nrow(batch))[1:nrow(batch)],
stringsAsFactors = FALSE)
colnames(batch) <-
c("File.Name", "Sample.ID", "Position")
temp.class <- sort(rep(1:nrow(batch), QCstep))
temp.class <- temp.class[1:nrow(batch)]
batch <-
data.frame(temp.class, batch, stringsAsFactors = FALSE)
batch <-
plyr::dlply(.data = batch,
.variables = plyr::.(temp.class))
batch <- lapply(batch, function(x) {
rbind(blank.qc, x[, -1, drop = FALSE])
})
batch <- do.call(rbind, batch)
batch <- rbind(batch, blank.qc)
rownames(batch) <- NULL
batch.pos <- data.frame(batch,
Path = paste(dir, "POS", sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""))
batch.neg <- data.frame(batch,
Path = paste(dir, "NEG", sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""))
batch.pos <-
batch.pos[, c("File.Name", "Sample.ID", "Path", "Instrument.Method", "Position")]
batch.neg <-
batch.neg[, c("File.Name", "Sample.ID", "Path", "Instrument.Method", "Position")]
condition.qc.pos <- data.frame(
condition.qc,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""),
stringsAsFactors = FALSE
)
condition.qc.neg <- data.frame(
condition.qc,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""),
stringsAsFactors = FALSE
)
blank.pos <- data.frame(blank,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""),
stringsAsFactors = FALSE
)
blank.neg <- data.frame(blank,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""),
stringsAsFactors = FALSE
)
dilution.qc.pos <- data.frame(
dilution.qc,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""),
stringsAsFactors = FALSE
)
dilution.qc.neg <- data.frame(
dilution.qc,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""),
stringsAsFactors = FALSE
)
ms2.qc.pos <- data.frame(
ms2.qc,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms2.method.pos, sep = ""),
stringsAsFactors = FALSE
)
ms2.qc.neg <- data.frame(
ms2.qc,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms2.method.neg, sep = ""),
stringsAsFactors = FALSE
)
condition.qc.pos <- condition.qc.pos[, colnames(batch.pos)]
condition.qc.neg <- condition.qc.neg[, colnames(batch.neg)]
blank.pos <- blank.pos[, colnames(batch.pos)]
blank.neg <- blank.neg[, colnames(batch.neg)]
dilution.qc.pos <- dilution.qc.pos[, colnames(batch.pos)]
dilution.qc.neg <- dilution.qc.neg[, colnames(batch.neg)]
ms2.qc.pos <- ms2.qc.pos[, colnames(batch.pos)]
ms2.qc.neg <- ms2.qc.neg[, colnames(batch.neg)]
batch.pos <- rbind(condition.qc.pos, dilution.qc.pos, ms2.qc.pos, batch.pos, blank.pos)
batch.neg <- rbind(condition.qc.neg, dilution.qc.neg, ms2.qc.neg, batch.neg, blank.neg)
###rename
batch.pos[which(batch.pos[, 1] == "Condition.QC"), 1] <-
paste(batch.pos[which(batch.pos[, 1] == "Condition.QC"), 1],
1:length(which(batch.pos[, 1] == "Condition.QC")), sep = "_")
batch.pos[which(batch.pos[, 1] == "QC"), 1] <-
paste("QC", qc.index.from:(sum(batch.pos[, 1] == "QC") + qc.index.from-1),
sep = "_")
batch.pos[which(batch.pos[, 1] == "Blank"), 1] <-
paste(batch.pos[which(batch.pos[, 1] == "Blank"), 1],
1:length(which(batch.pos[, 1] == "Blank")), sep = "_")
batch.pos[, 2] <- batch.pos[, 1]
batch.neg[which(batch.neg[, 1] == "Condition.QC"), 1] <-
paste(batch.neg[which(batch.neg[, 1] == "Condition.QC"), 1],
1:length(which(batch.neg[, 1] == "Condition.QC")), sep = "_")
batch.neg[which(batch.neg[, 1] == "QC"), 1] <-
paste("QC", qc.index.from:(sum(batch.neg[, 1] == "QC") + qc.index.from-1),
sep = "_")
batch.neg[which(batch.neg[, 1] == "Blank"), 1] <-
paste(batch.neg[which(batch.neg[, 1] == "Blank"), 1],
1:length(which(batch.neg[, 1] == "Blank")), sep = "_")
batch.neg[, 2] <- batch.neg[, 1]
write.csv(batch.pos, "worklist.pos.csv", row.names = FALSE)
write.csv(batch.neg, "worklist.neg.csv", row.names = FALSE)
# each.mode.number <-
# ceiling(each.mode.number / QCstep) * (QCstep + 2)
#
# temp.class <-
# sort(rep(1:nrow(batch.pos), each.mode.number))
# temp.class <- temp.class[1:nrow(batch.pos)]
#
# batch.pos <- data.frame(temp.class, batch.pos,
# stringsAsFactors = FALSE)
#
# batch.neg <- data.frame(temp.class, batch.neg,
# stringsAsFactors = FALSE)
#
# batch.pos <-
# plyr::dlply(.data = batch.pos,
# .variables = plyr::.(temp.class))
#
# batch.neg <-
# plyr::dlply(.data = batch.neg,
# .variables = plyr::.(temp.class))
#
# batch <- mapply(
# FUN = function(x, y) {
# list(rbind(x, y))
# },
# x = batch.pos,
# y = batch.neg
# )
#
# batch <- do.call(rbind, batch)
#
# rownames(batch) <- NULL
# batch <- batch[, -1, drop = FALSE]
#
# condition.qc <- data.frame(
# condition.qc,
# "Path" = paste(dir, 'POS', sep = ""),
# stringsAsFactors = FALSE
# )
#
# blank <- data.frame(blank,
# "Path" = paste(dir, 'NEG', sep = ""),
# stringsAsFactors = FALSE)
#
# condition.qc <- condition.qc[, colnames(batch)]
# blank <- blank[, colnames(batch)]
#
# batch <- rbind(condition.qc, batch, blank)
#
#
# ###rename
# batch[which(batch[, 1] == "Condition.QC"), 1] <-
# paste(batch[which(batch[, 1] == "Condition.QC"), 1],
# 1:length(which(batch[, 1] == "Condition.QC")), sep = "_")
#
# batch[which(batch[, 1] == "QC"), 1] <-
# paste(batch[which(batch[, 1] == "QC"), 1],
# 1:length(which(batch[, 1] == "QC")), sep = "_")
#
# batch[which(batch[, 1] == "Blank"), 1] <-
# paste(batch[which(batch[, 1] == "Blank"), 1],
# 1:length(which(batch[, 1] == "Blank")), sep = "_")
#
# batch[, 2] <- batch[, 1]
#
# write.csv(batch, "worklist.csv", row.names = FALSE)
}
}
}
)
jaspershen/sxtTools documentation built on May 2, 2020, 6:37 a.m.
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#' @title getWorklist
#' @description Generate Worklist for MS data acquisition.
#' @author Xiaotao Shen
#' \email{shenxt@@sioc.ac.cn}
#' @param instrument Which instrument you use?
#' "Agilent", "AB" or "Thermo", default is "Thermo".
#' @param name The name of worklist.
#' @param randommethod Which random method you want to use?
#' "no", "position" or "injection". Default is "no".
#' @param samplenumber Sample number.
#' @param replication Replication times.
#' @param QCstep QC step.
#' @param conditionQCnumber Condition QC number.
#' @param validationQCstep Validation QC step.
#' @param testmixstep Test mixture step.
#' @param injectionfrom Injection order from which? Default is 1.
#' @param user Default is "other".
#' @param dir Directory.
#' @return New worklist.
#' @export
setGeneric(
name = "getWorklist",
def = function(table.name = "batch1.xlsx",
instrument = c("Thermo", "Agilent", "AB"),
each.mode.number = 30,
randommethod = c("no", "position", "injection"),
samplenumber = NULL,
replication = 1,
QCstep = 8,
conditionQCnumber = 5,
qc.index.from = 1,
dir = "D:\\Liang\\SmarD_Urine_20190731\\RPLC\\",
method.path = "D:\\Liang\\Methods\\RPLC\\Urine\\",
ms1.method.pos = "Hypersil_GOLD_MS_pos",
ms1.method.neg = "Hypersil_GOLD_MS_neg",
ms2.method.pos = c("Hypersil_GOLD_MSMS_pos_NCE25_70_250",
"Hypersil_GOLD_MSMS_pos_NCE25_240_400",
"Hypersil_GOLD_MSMS_pos_NCE25_390_600",
"Hypersil_GOLD_MSMS_pos_NCE25_590_1000",
"Hypersil_GOLD_MSMS_pos_NCE50_70_250",
"Hypersil_GOLD_MSMS_pos_NCE50_240_400",
"Hypersil_GOLD_MSMS_pos_NCE50_390_600",
"Hypersil_GOLD_MSMS_pos_NCE50_590_1000"),
ms2.method.neg = c("Hypersil_GOLD_MSMS_neg_NCE25_70_250",
"Hypersil_GOLD_MSMS_neg_NCE25_240_400",
"Hypersil_GOLD_MSMS_neg_NCE25_390_600",
"Hypersil_GOLD_MSMS_neg_NCE25_590_1000",
"Hypersil_GOLD_MSMS_neg_NCE50_70_250",
"Hypersil_GOLD_MSMS_neg_NCE50_240_400",
"Hypersil_GOLD_MSMS_neg_NCE50_390_600",
"Hypersil_GOLD_MSMS_neg_NCE50_590_1000")
) {
instrument <- match.arg(instrument)
randommethod <- match.arg(randommethod)
options(warn = -1)
file <- dir()
if (instrument == "Thermo") {
batch <- readxl::read_excel(table.name)
if (randommethod == "no") {
###add position
position <-
unlist(lapply(c("B", "G", "R"), function(y) {
paste(y,
unlist(lapply(LETTERS[1:5], function(x) {
paste(x, 1:8, sep = "")
})),
sep = "")
}))
position <- position[-c(1:8)]
condition.qc <-
matrix(rep(
c("Condition.QC", 'Condition.QC', "BA1"),
conditionQCnumber
),
ncol = 3,
byrow = TRUE)
condition.qc <-
as.data.frame(condition.qc, stringsAsFactors = FALSE)
colnames(condition.qc) <-
c("File.Name", "Sample.ID", 'Position')
blank.qc <-
data.frame(
"File.Name" = c("Blank", "QC"),
"Sample.ID" = c("Blank", "QC"),
"Position" = c("BA2", "BA1"),
stringsAsFactors = FALSE
)
blank <-
data.frame(
"File.Name" = c("Blank", "Blank", "Blank"),
"Sample.ID" = c("Blank", "Blank", "Blank"),
"Position" = c("BA2", "BA2", "BA2"),
stringsAsFactors = FALSE
)
dilution.qc <- data.frame(
"File.Name" = c("DL_QC1_1", "DL_QC2_1", "DL_QC4_1", "DL_QC8_1", "DL_QC1_2", "DL_QC2_2", "DL_QC4_2", "DL_QC8_2"),
"Sample.ID" = c("DL_QC1_1", "DL_QC2_1", "DL_QC4_1", "DL_QC8_1", "DL_QC1_2", "DL_QC2_2", "DL_QC4_2", "DL_QC8_2"),
"Position" = c("BA3", "BA4", "BA5", "BA6", "BA3", "BA4", "BA5", "BA6"),
stringsAsFactors = FALSE
)
ms2.qc <-
data.frame(
"File.Name" = c("QC_MS2_NCE25_1", "QC_MS2_NCE25_2", "QC_MS2_NCE25_3", "QC_MS2_NCE25_4",
"QC_MS2_NCE50_1", "QC_MS2_NCE50_2", "QC_MS2_NCE50_3", "QC_MS2_NCE50_4"),
"Sample.ID" = c("QC_MS2_NCE25_1", "QC_MS2_NCE25_2", "QC_MS2_NCE25_3", "QC_MS2_NCE25_4",
"QC_MS2_NCE50_1", "QC_MS2_NCE50_2", "QC_MS2_NCE50_3", "QC_MS2_NCE50_4"),
"Position" = c("BA1", "BA1", "BA1", "BA1", "BA1", "BA1", "BA1", "BA1"),
stringsAsFactors = FALSE
)
batch <- cbind(batch, batch)
batch <- data.frame(batch,
"Position" = rep(position, nrow(batch))[1:nrow(batch)],
stringsAsFactors = FALSE)
colnames(batch) <-
c("File.Name", "Sample.ID", "Position")
temp.class <- sort(rep(1:nrow(batch), QCstep))
temp.class <- temp.class[1:nrow(batch)]
batch <-
data.frame(temp.class, batch, stringsAsFactors = FALSE)
batch <-
plyr::dlply(.data = batch,
.variables = plyr::.(temp.class))
batch <- lapply(batch, function(x) {
rbind(blank.qc, x[, -1, drop = FALSE])
})
batch <- do.call(rbind, batch)
batch <- rbind(batch, blank.qc)
rownames(batch) <- NULL
batch.pos <- data.frame(batch,
Path = paste(dir, "POS", sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""))
batch.neg <- data.frame(batch,
Path = paste(dir, "NEG", sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""))
batch.pos <-
batch.pos[, c("File.Name", "Sample.ID", "Path", "Instrument.Method", "Position")]
batch.neg <-
batch.neg[, c("File.Name", "Sample.ID", "Path", "Instrument.Method", "Position")]
condition.qc.pos <- data.frame(
condition.qc,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""),
stringsAsFactors = FALSE
)
condition.qc.neg <- data.frame(
condition.qc,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""),
stringsAsFactors = FALSE
)
blank.pos <- data.frame(blank,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""),
stringsAsFactors = FALSE
)
blank.neg <- data.frame(blank,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""),
stringsAsFactors = FALSE
)
dilution.qc.pos <- data.frame(
dilution.qc,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms1.method.pos, sep = ""),
stringsAsFactors = FALSE
)
dilution.qc.neg <- data.frame(
dilution.qc,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms1.method.neg, sep = ""),
stringsAsFactors = FALSE
)
ms2.qc.pos <- data.frame(
ms2.qc,
"Path" = paste(dir, 'POS', sep = ""),
Instrument.Method = paste(method.path, ms2.method.pos, sep = ""),
stringsAsFactors = FALSE
)
ms2.qc.neg <- data.frame(
ms2.qc,
"Path" = paste(dir, 'NEG', sep = ""),
Instrument.Method = paste(method.path, ms2.method.neg, sep = ""),
stringsAsFactors = FALSE
)
condition.qc.pos <- condition.qc.pos[, colnames(batch.pos)]
condition.qc.neg <- condition.qc.neg[, colnames(batch.neg)]
blank.pos <- blank.pos[, colnames(batch.pos)]
blank.neg <- blank.neg[, colnames(batch.neg)]
dilution.qc.pos <- dilution.qc.pos[, colnames(batch.pos)]
dilution.qc.neg <- dilution.qc.neg[, colnames(batch.neg)]
ms2.qc.pos <- ms2.qc.pos[, colnames(batch.pos)]
ms2.qc.neg <- ms2.qc.neg[, colnames(batch.neg)]
batch.pos <- rbind(condition.qc.pos, dilution.qc.pos, ms2.qc.pos, batch.pos, blank.pos)
batch.neg <- rbind(condition.qc.neg, dilution.qc.neg, ms2.qc.neg, batch.neg, blank.neg)
###rename
batch.pos[which(batch.pos[, 1] == "Condition.QC"), 1] <-
paste(batch.pos[which(batch.pos[, 1] == "Condition.QC"), 1],
1:length(which(batch.pos[, 1] == "Condition.QC")), sep = "_")
batch.pos[which(batch.pos[, 1] == "QC"), 1] <-
paste("QC", qc.index.from:(sum(batch.pos[, 1] == "QC") + qc.index.from-1),
sep = "_")
batch.pos[which(batch.pos[, 1] == "Blank"), 1] <-
paste(batch.pos[which(batch.pos[, 1] == "Blank"), 1],
1:length(which(batch.pos[, 1] == "Blank")), sep = "_")
batch.pos[, 2] <- batch.pos[, 1]
batch.neg[which(batch.neg[, 1] == "Condition.QC"), 1] <-
paste(batch.neg[which(batch.neg[, 1] == "Condition.QC"), 1],
1:length(which(batch.neg[, 1] == "Condition.QC")), sep = "_")
batch.neg[which(batch.neg[, 1] == "QC"), 1] <-
paste("QC", qc.index.from:(sum(batch.neg[, 1] == "QC") + qc.index.from-1),
sep = "_")
batch.neg[which(batch.neg[, 1] == "Blank"), 1] <-
paste(batch.neg[which(batch.neg[, 1] == "Blank"), 1],
1:length(which(batch.neg[, 1] == "Blank")), sep = "_")
batch.neg[, 2] <- batch.neg[, 1]
write.csv(batch.pos, "worklist.pos.csv", row.names = FALSE)
write.csv(batch.neg, "worklist.neg.csv", row.names = FALSE)
# each.mode.number <-
# ceiling(each.mode.number / QCstep) * (QCstep + 2)
#
# temp.class <-
# sort(rep(1:nrow(batch.pos), each.mode.number))
# temp.class <- temp.class[1:nrow(batch.pos)]
#
# batch.pos <- data.frame(temp.class, batch.pos,
# stringsAsFactors = FALSE)
#
# batch.neg <- data.frame(temp.class, batch.neg,
# stringsAsFactors = FALSE)
#
# batch.pos <-
# plyr::dlply(.data = batch.pos,
# .variables = plyr::.(temp.class))
#
# batch.neg <-
# plyr::dlply(.data = batch.neg,
# .variables = plyr::.(temp.class))
#
# batch <- mapply(
# FUN = function(x, y) {
# list(rbind(x, y))
# },
# x = batch.pos,
# y = batch.neg
# )
#
# batch <- do.call(rbind, batch)
#
# rownames(batch) <- NULL
# batch <- batch[, -1, drop = FALSE]
#
# condition.qc <- data.frame(
# condition.qc,
# "Path" = paste(dir, 'POS', sep = ""),
# stringsAsFactors = FALSE
# )
#
# blank <- data.frame(blank,
# "Path" = paste(dir, 'NEG', sep = ""),
# stringsAsFactors = FALSE)
#
# condition.qc <- condition.qc[, colnames(batch)]
# blank <- blank[, colnames(batch)]
#
# batch <- rbind(condition.qc, batch, blank)
#
#
# ###rename
# batch[which(batch[, 1] == "Condition.QC"), 1] <-
# paste(batch[which(batch[, 1] == "Condition.QC"), 1],
# 1:length(which(batch[, 1] == "Condition.QC")), sep = "_")
#
# batch[which(batch[, 1] == "QC"), 1] <-
# paste(batch[which(batch[, 1] == "QC"), 1],
# 1:length(which(batch[, 1] == "QC")), sep = "_")
#
# batch[which(batch[, 1] == "Blank"), 1] <-
# paste(batch[which(batch[, 1] == "Blank"), 1],
# 1:length(which(batch[, 1] == "Blank")), sep = "_")
#
# batch[, 2] <- batch[, 1]
#
# write.csv(batch, "worklist.csv", row.names = FALSE)
}
}
}
)
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