R/classRequestList.r
In jwist/request: What the Package Does (One Line, Title Case)
#' request list class
#' @slot entry - a list of requests
#' @export
setClass("requestList",
representation = representation(entry = "list"),
prototype(entry = list()),
contains = list("list")
)
#' adding request to list
#' @param r - the request list
#' @param entry - the new request
#' @export
setGeneric("addRequest", function(r, entry) {
standardGeneric("addRequest")
})
#' adding request to list
#' @param r - the request list
#' @param entry - the new request
#' @export
setMethod("addRequest",
c(r = "requestList", entry = "list"),
function(r, entry) {
r@entry <- c(r@entry, entry)
return(r)
}
)
#' printing a request list
#' @param r - the request list
#' @param options - options
#' @export
setGeneric("printRequest", function(r, options) {
standardGeneric("printRequest")
})
#' printing a request list
#' @param r - the request list
#' @param options - options
#' @export
setMethod("printRequest",
c(r = "requestList", options = "list"),
function(r, options) {
rlist <- list()
for (j in 1:length(r@entry)) {
i <- r@entry[[j]]
row <- LETTERS[1:8]
if (options$assay == "MSBruker") {
# path <- "D:\\Data\\AA Methods\\Amino Acid\\"
path <- paste0("D:\\lims\\", i@projectName, "\\Amino Acid\\")
# methSet <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid MethodSet VALIDATED.m"
sepMeth <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid LC method VALIDATED.m?HyStar_LC"
MSMeth <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid MS method VALIDATED.m?microTOFQImpactControl"
procMeth <- "D:\\Methods\\Amino Acid VALIDATED\\NaFA pos recal readout.m?DataAnalysis"
injMeth <- "Standard"
calLev <- switch(i@sampleID,
"CAL08" = 1,
"CAL07" = 2,
"CAL06" = 4,
"CAL05" = 10,
"CAL04" = 20,
"CAL03" = 100,
"CAL02" = 200,
"CAL01" = 400,
"QC04" = 3,
"QC03" = 15,
"QC02" = 75,
"QC01" = 300)
if (is.null(calLev)) { calLev <- 0}
if (i@row == 0){
sampleLocation <- "V:1"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
# "Method Set" = methSet,
"Separation Method" = sepMeth,
"MS Method" = MSMeth,
"Processing Method" = procMeth,
"injMeth" = injMeth,
"Sample Type" = i@sampleType,
"Calib. Level" = calLev,
"Inj." = 1,
#"Volume [µl]" = 2,
"Volume" = 2,
"Data Path" = path,
"Run Automated Processing" = "true", check.names = FALSE)
} else if (options$assay == "MSWaters") {
msFile <- "2020_Tryptophan_v5_0_AD"
msTunFile <- "2020_Tryptophan_v1_0"
inletFile <- "2020_Tryptophan_v1_0"
injVol <- 10
if (i@row == 0){
sampleLocation <- "V:1"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
if ("conc" %in% names(i@options)){
calLev = i@options$conc
} else {
calLev = rep("", 9)
}
rlist[[j]] <- data.frame("Index" = "",
"FILE_NAME" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"INJ_VOL" = injVol,
"TYPE" = i@sampleType,
"SAMPLE_LOCATION" = sampleLocation,
"INLET_FILE" = inletFile,
"MS_TUNE_FILE" = msTunFile,
"MS_FILE" = msFile,
"FILE_TEXT" = gsub("\\.", "_", i@sampleID),
"CONC_A" = calLev[1],
"CONC_B" = calLev[2],
"CONC_C" = calLev[3],
"CONC_D" = calLev[4],
"CONC_E" = calLev[5],
"CONC_F" = calLev[6],
"CONC_G" = calLev[7],
"CONC_H" = calLev[8],
"CONC_I" = calLev[9], check.names = FALSE)
} else if (options$assay == "MS-TRYE") {
methodName <- "Tryptophan_method_optimization"
injVol <- 20
# if (i@row == 0){
# sampleLocation <- "V:1"
# } else if (i@row == -1) {
# sampleLocation <- "V:4"
# } else {
sampleLocation <- RCToPos(i@row, i@column) #paste0(i@platePosition, ":", row[i@row], ",", i@column)
# }
if (i@platePosition == 1) {
plateLocation <- "Left"
} else if (i@platePosition == 2) {
plateLocation <- "Right"
}
calLev <- switch(i@sampleID,
"CAL08" = 1,
"CAL07" = 2,
"CAL06" = 4,
"CAL05" = 10,
"CAL04" = 20,
"CAL03" = 100,
"CAL02" = 200,
"CAL01" = 400,
"QC04" = 3,
"QC03" = 15,
"QC02" = 75,
"QC01" = 300)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("Sample Position" = sampleLocation,
"Sample Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"Sample Type" = i@sampleType,
"Concentration Level" = calLev,
"Injection Volume" = injVol,
"Method Name" = methodName,
"Plate" = plateLocation,
"Comment" = NA,
"Dilution" = 1, check.names = FALSE)
} else if (options$assay == "MS-BILEE") {
methodName <- "1062022_BileAcids_direct_compare"
injVol <- 20
# if (i@row == 0){
# sampleLocation <- "V:1"
# } else if (i@row == -1) {
# sampleLocation <- "V:4"
# } else {
sampleLocation <- RCToPos(i@row, i@column) #paste0(i@platePosition, ":", row[i@row], ",", i@column)
# }
if (i@platePosition == 1) {
plateLocation <- "Left"
} else if (i@platePosition == 2) {
plateLocation <- "Right"
}
calLev <- switch(i@sampleID,
"CAL08" = 0.5,
"CAL07" = 2,
"CAL06" = 10,
"CAL05" = 50,
"CAL04" = 150,
"CAL03" = 600,
"CAL02" = 1200,
"CAL01" = 2000,
"QC04" = 5,
"QC03" = 80,
"QC02" = 800,
"QC01" = 2000)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("Sample Position" = sampleLocation,
"Sample Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"Sample Type" = i@sampleType,
"Concentration Level" = calLev,
"Injection Volume" = injVol,
"Method Name" = methodName,
"Plate" = plateLocation,
"Comment" = NA,
"Dilution" = 1, check.names = FALSE)
} else if (options$assay == "MS-BILE") {
msFile <- "BileAcids_MS_2022"
msTunFile <- "BileAcids_Tune_2022"
inletFile <- "BileAcids_LC_2022"
injVol <- 5
if (i@row == 0){
sampleLocation <- "2:F,8"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
calLev <- switch(i@sampleID,
"CAL08" = 5,
"CAL07" = 15,
"CAL06" = 25,
"CAL05" = 75,
"CAL04" = 150,
"CAL03" = 300,
"CAL02" = 600,
"CAL01" = 1000,
"QC04" = 8,
"QC03" = 32,
"QC02" = 320,
"QC01" = 800)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("File Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"INLET_FILE" = inletFile,
"MS_TUNE_FILE" = msTunFile,
"MS_FILE" = msFile,
"SAMPLE_LOCATION" = sampleLocation,
"INJ_VOL" = injVol,
"TYPE" = i@sampleType,
"CONC_A" = calLev, check.names = FALSE)
} else if (options$assay == "MS-Q300") {
msFile <- "Q300-ver1"
msTunFile <- "Q300_20210316"
inletFile <- "20210209-Q300-1"
injVol <- 5
if (i@row == 0){
sampleLocation <- "V:1"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
calLev <- switch(i@sampleID,
"CAL08" = NA,
"CAL07" = NA,
"CAL06" = NA,
"CAL05" = NA,
"CAL04" = NA,
"CAL03" = NA,
"CAL02" = NA,
"CAL01" = NA)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("File Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"INLET_FILE" = inletFile,
"MS_TUNE_FILE" = msTunFile,
"MS_FILE" = msFile,
"SAMPLE_LOCATION" = sampleLocation,
"INJ_VOL" = injVol,
"TYPE" = i@sampleType,
"CONC_A" = calLev, check.names = FALSE)
} else if (options$assay == "MSSciex") {
rackPos <- i@platePosition
smplInjVol <- 5
acqMethod <- "LM_RP_sMRM_LIPIDS"
rackCode <- "Rack Order (Column)"
plateCode <- "MTP 96"
platePos <- i@platePosition
if (i@row > 0){
sampleLocation <- RCToNum(i@row, i@column)
} else if (i@row == -1) {
sampleLocation <- "20001"
} else {
sampleLocation <- NA
}
rlist[[j]] <- data.frame("% header=SampleName" = paste0(i@sampleID, "_", j),
"SampleId" = paste0(i@sampleID, "_", j),
"RackCode" = rackCode,
"Rackpos" = rackPos,
"PlateCode" = plateCode,
"SmplInjVol" = smplInjVol,
"AcqMethod" = acqMethod,
"PlatePos" = platePos,
"VialPos" = sampleLocation,
"OutputFile" = i@runName,
"Type" = i@sampleType,
check.names = FALSE)
} else if (options$assay == "MS_EICOS") {
rackPos <- 1
smplInjVol <- 5
acqMethod <- "Eicosanoids_Quantitation-2021"
rackCode <- "Rack Order (Column)"
plateCode <- "MTP 96"
platePos <- i@platePosition
if (i@row > 0){
sampleLocation <- RCToNum(i@row, i@column)
} else {
sampleLocation <- 20001
}
rlist[[j]] <- data.frame("SampleName" = paste0(i@sampleID, "_", j),
"Rack Code" = rackCode,
"Rack position" = rackPos,
"Plate Code" = plateCode,
"PlatePos" = platePos,
"VialPos" = sampleLocation,
"Acquisition Method" = acqMethod,
"Data File" = i@runName,
"Injection Volume" = smplInjVol,
check.names = FALSE)
} else if (options$assay == "MS_URPP") {
path <- paste0("D:\\lims\\", i@projectName, "\\URPP\\")
methSet <- "D:\\Methods\\URPP\\URPP VALIDATED.m"
if (i@row == 0){
col <- (i@column %% 4) + 1
sampleLocation <- paste0("V:", col)
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Sample Type" = i@sampleType,
"Calib. Level" = 0,
"Inj." = 1,
"Volume" = 2,
"Data Path" = path,
"Run Automated Processing" = "true", check.names = FALSE)
} else if (options$assay == "MS_MRMSP") {
path <- paste0("D:\\lims\\", i@projectName, "\\MRMSP\\")
methSet <- "D:\\Methods\\FIA_Methods\\200802_Hexakis_Lockmass.m"
sepMeth <- "D:\\Methods\\FIA_Methods\\201217_LC_method.m"
msMeth <- "D:\\Methods\\FIA_Methods\\201217_MRMS_POS.m"
rlist[[j]] <- data.frame("Vial" = paste0(1, ":", i@platePosition, ":", RCToNum(i@row, i@column)),
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"MS Method" = msMeth,
"Sample Type" = i@sampleType,
"Volume [µl]" = 20,
"Data Path" = path,
"Result Path" = "", check.names = FALSE)
} else if (options$assay == "MS_MRMSN") {
# path <- "D:\\Data\\AA Methods\\Amino Acid\\"
path <- paste0("D:\\lims\\", i@projectName, "\\MRMSN\\")
methSet <- "D:\\Methods\\FIA_Methods\\200802_Hexakis_Lockmass.m"
sepMeth <- "D:\\Methods\\FIA_Methods\\201217_LC_method.m"
msMeth <- "D:\\Methods\\FIA_Methods\\201217_MRMS_NEG.m"
rlist[[j]] <- data.frame("Vial" = paste0(1, ":", i@platePosition, ":", RCToNum(i@row, i@column)),
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"MS Method" = msMeth,
"Sample Type" = i@sampleType,
"Volume [µl]" = 20,
"Data Path" = path,
"Result Path" = "", check.names = FALSE)
} else if (options$assay == "TIMS_LIPIDS_N") {
path <- paste0("D:\\lims\\", i@projectName, "\\TIMS_LIPIDS_N\\")
methSet <- ""
sepMeth <- "D:\\Methods\\CORTECS\ T3\ Lipidomics\\2020\ 0921_CORTECS\ T3_A2B2_Lipidomics_400uLmin_15min_PLNO_v1.m"
msMeth <- "D:\\Methods\\CRC-lipid_CSH_C18\\2020 0831-4D-Lipidomics_ANPC_v1.m"
procMeth <- "D:\\Data\\NaFA\ pos\ recal\ readout.m"
injMeth <- "Standard"
if (i@platePosition == 0){
sampleLocation <- paste0("V:", i@row)
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"Injection Method" = injMeth,
"MS Method" = msMeth,
"Processing Method" = procMeth,
"Sample Type" = i@sampleType,
"Inj." = 1,
"Volume [µl]" = 7.5,
"Data Path" = path,
"Run Automated Processing" = "TRUE", check.names = FALSE)
} else if (options$assay == "TIMS_LIPIDS_P") {
path <- paste0("D:\\lims\\", i@projectName, "\\TIMS_LIPIDS_P\\")
methSet <- ""
sepMeth <- "D:\\Methods\\CORTECS\ T3\ Lipidomics\\2020\ 0921_CORTECS\ T3_A2B2_Lipidomics_400uLmin_15min_PLNO_v1.m"
msMeth <- "D:\\Methods\\CRC-lipid_CSH_C18\\2020 0831-4D-Lipidomics_ANPC_v1.m"
procMeth <- "D:\\Data\\NaFA\ pos\ recal\ readout.m"
injMeth <- "Standard"
if (i@platePosition == 0){
sampleLocation <- paste0("V:", i@row)
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"Injection Method" = injMeth,
"MS Method" = msMeth,
"Processing Method" = procMeth,
"Sample Type" = i@sampleType,
"Inj." = 1,
"Volume [µl]" = 7.5,
"Data Path" = path,
"Run Automated Processing" = "TRUE", check.names = FALSE)
} else {
rlist[[j]] <- data.frame("_sampleID" = i@sampleID,
"_matrixID" = i@matrixID,
"_runName" = i@runName,
"_sampleType" = i@sampleType,
"_methodID" = i@methodID,
"_deviceID" = i@deviceID,
"_projectName" = i@projectName,
"_platePosition" = i@platePosition,
"row" = i@row,
"column" = i@column, check.names = FALSE)
}
df <- do.call("rbind", rlist)
}
# adding shutdown blank
if (options$assay == "MSBruker") {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
path <- "D:\\Methods\\System startup\\LC Methods\\"
methSet <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid LC method SHUTDOWN.m"
sepMeth <- "Amino acid LC method SHUTDOWN"
injMeth <- "Standard"
MSMeth <- ""
procMeth <- ""
df$`Sample ID`[last] <- paste0(i@runName, "_Blank Shutdown_", last)
df$`Separation Method`[last] <- sepMeth
} else if (options$assay == "MSWaters") {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
inletFile <- "AAA end"
df$`INLET_FILE`[last] <- inletFile
df$`FILE_TEXT`[last] <- "Blank Shutdown"
df$`TYPE`[last] <- "Blank"
df$FILE_NAME[last] <- paste0(i@runName, "_BlankShutdown_", last)
} else if (options$assay == "MS-BILE") {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
df$`File Name`[last] <- paste0(i@runName, "_BlankShutdown_", last)
} else {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
}
return(df)
}
)
jwist/request documentation built on Aug. 10, 2022, 4:11 p.m.
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#' request list class
#' @slot entry - a list of requests
#' @export
setClass("requestList",
representation = representation(entry = "list"),
prototype(entry = list()),
contains = list("list")
)
#' adding request to list
#' @param r - the request list
#' @param entry - the new request
#' @export
setGeneric("addRequest", function(r, entry) {
standardGeneric("addRequest")
})
#' adding request to list
#' @param r - the request list
#' @param entry - the new request
#' @export
setMethod("addRequest",
c(r = "requestList", entry = "list"),
function(r, entry) {
r@entry <- c(r@entry, entry)
return(r)
}
)
#' printing a request list
#' @param r - the request list
#' @param options - options
#' @export
setGeneric("printRequest", function(r, options) {
standardGeneric("printRequest")
})
#' printing a request list
#' @param r - the request list
#' @param options - options
#' @export
setMethod("printRequest",
c(r = "requestList", options = "list"),
function(r, options) {
rlist <- list()
for (j in 1:length(r@entry)) {
i <- r@entry[[j]]
row <- LETTERS[1:8]
if (options$assay == "MSBruker") {
# path <- "D:\\Data\\AA Methods\\Amino Acid\\"
path <- paste0("D:\\lims\\", i@projectName, "\\Amino Acid\\")
# methSet <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid MethodSet VALIDATED.m"
sepMeth <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid LC method VALIDATED.m?HyStar_LC"
MSMeth <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid MS method VALIDATED.m?microTOFQImpactControl"
procMeth <- "D:\\Methods\\Amino Acid VALIDATED\\NaFA pos recal readout.m?DataAnalysis"
injMeth <- "Standard"
calLev <- switch(i@sampleID,
"CAL08" = 1,
"CAL07" = 2,
"CAL06" = 4,
"CAL05" = 10,
"CAL04" = 20,
"CAL03" = 100,
"CAL02" = 200,
"CAL01" = 400,
"QC04" = 3,
"QC03" = 15,
"QC02" = 75,
"QC01" = 300)
if (is.null(calLev)) { calLev <- 0}
if (i@row == 0){
sampleLocation <- "V:1"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
# "Method Set" = methSet,
"Separation Method" = sepMeth,
"MS Method" = MSMeth,
"Processing Method" = procMeth,
"injMeth" = injMeth,
"Sample Type" = i@sampleType,
"Calib. Level" = calLev,
"Inj." = 1,
#"Volume [µl]" = 2,
"Volume" = 2,
"Data Path" = path,
"Run Automated Processing" = "true", check.names = FALSE)
} else if (options$assay == "MSWaters") {
msFile <- "2020_Tryptophan_v5_0_AD"
msTunFile <- "2020_Tryptophan_v1_0"
inletFile <- "2020_Tryptophan_v1_0"
injVol <- 10
if (i@row == 0){
sampleLocation <- "V:1"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
if ("conc" %in% names(i@options)){
calLev = i@options$conc
} else {
calLev = rep("", 9)
}
rlist[[j]] <- data.frame("Index" = "",
"FILE_NAME" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"INJ_VOL" = injVol,
"TYPE" = i@sampleType,
"SAMPLE_LOCATION" = sampleLocation,
"INLET_FILE" = inletFile,
"MS_TUNE_FILE" = msTunFile,
"MS_FILE" = msFile,
"FILE_TEXT" = gsub("\\.", "_", i@sampleID),
"CONC_A" = calLev[1],
"CONC_B" = calLev[2],
"CONC_C" = calLev[3],
"CONC_D" = calLev[4],
"CONC_E" = calLev[5],
"CONC_F" = calLev[6],
"CONC_G" = calLev[7],
"CONC_H" = calLev[8],
"CONC_I" = calLev[9], check.names = FALSE)
} else if (options$assay == "MS-TRYE") {
methodName <- "Tryptophan_method_optimization"
injVol <- 20
# if (i@row == 0){
# sampleLocation <- "V:1"
# } else if (i@row == -1) {
# sampleLocation <- "V:4"
# } else {
sampleLocation <- RCToPos(i@row, i@column) #paste0(i@platePosition, ":", row[i@row], ",", i@column)
# }
if (i@platePosition == 1) {
plateLocation <- "Left"
} else if (i@platePosition == 2) {
plateLocation <- "Right"
}
calLev <- switch(i@sampleID,
"CAL08" = 1,
"CAL07" = 2,
"CAL06" = 4,
"CAL05" = 10,
"CAL04" = 20,
"CAL03" = 100,
"CAL02" = 200,
"CAL01" = 400,
"QC04" = 3,
"QC03" = 15,
"QC02" = 75,
"QC01" = 300)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("Sample Position" = sampleLocation,
"Sample Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"Sample Type" = i@sampleType,
"Concentration Level" = calLev,
"Injection Volume" = injVol,
"Method Name" = methodName,
"Plate" = plateLocation,
"Comment" = NA,
"Dilution" = 1, check.names = FALSE)
} else if (options$assay == "MS-BILEE") {
methodName <- "1062022_BileAcids_direct_compare"
injVol <- 20
# if (i@row == 0){
# sampleLocation <- "V:1"
# } else if (i@row == -1) {
# sampleLocation <- "V:4"
# } else {
sampleLocation <- RCToPos(i@row, i@column) #paste0(i@platePosition, ":", row[i@row], ",", i@column)
# }
if (i@platePosition == 1) {
plateLocation <- "Left"
} else if (i@platePosition == 2) {
plateLocation <- "Right"
}
calLev <- switch(i@sampleID,
"CAL08" = 0.5,
"CAL07" = 2,
"CAL06" = 10,
"CAL05" = 50,
"CAL04" = 150,
"CAL03" = 600,
"CAL02" = 1200,
"CAL01" = 2000,
"QC04" = 5,
"QC03" = 80,
"QC02" = 800,
"QC01" = 2000)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("Sample Position" = sampleLocation,
"Sample Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"Sample Type" = i@sampleType,
"Concentration Level" = calLev,
"Injection Volume" = injVol,
"Method Name" = methodName,
"Plate" = plateLocation,
"Comment" = NA,
"Dilution" = 1, check.names = FALSE)
} else if (options$assay == "MS-BILE") {
msFile <- "BileAcids_MS_2022"
msTunFile <- "BileAcids_Tune_2022"
inletFile <- "BileAcids_LC_2022"
injVol <- 5
if (i@row == 0){
sampleLocation <- "2:F,8"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
calLev <- switch(i@sampleID,
"CAL08" = 5,
"CAL07" = 15,
"CAL06" = 25,
"CAL05" = 75,
"CAL04" = 150,
"CAL03" = 300,
"CAL02" = 600,
"CAL01" = 1000,
"QC04" = 8,
"QC03" = 32,
"QC02" = 320,
"QC01" = 800)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("File Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"INLET_FILE" = inletFile,
"MS_TUNE_FILE" = msTunFile,
"MS_FILE" = msFile,
"SAMPLE_LOCATION" = sampleLocation,
"INJ_VOL" = injVol,
"TYPE" = i@sampleType,
"CONC_A" = calLev, check.names = FALSE)
} else if (options$assay == "MS-Q300") {
msFile <- "Q300-ver1"
msTunFile <- "Q300_20210316"
inletFile <- "20210209-Q300-1"
injVol <- 5
if (i@row == 0){
sampleLocation <- "V:1"
} else if (i@row == -1) {
sampleLocation <- "V:4"
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
calLev <- switch(i@sampleID,
"CAL08" = NA,
"CAL07" = NA,
"CAL06" = NA,
"CAL05" = NA,
"CAL04" = NA,
"CAL03" = NA,
"CAL02" = NA,
"CAL01" = NA)
if (is.null(calLev)) { calLev <- 0}
rlist[[j]] <- data.frame("File Name" = paste0(i@runName,
"_",
gsub("\\.", "_", i@sampleID), "_",
j),
"INLET_FILE" = inletFile,
"MS_TUNE_FILE" = msTunFile,
"MS_FILE" = msFile,
"SAMPLE_LOCATION" = sampleLocation,
"INJ_VOL" = injVol,
"TYPE" = i@sampleType,
"CONC_A" = calLev, check.names = FALSE)
} else if (options$assay == "MSSciex") {
rackPos <- i@platePosition
smplInjVol <- 5
acqMethod <- "LM_RP_sMRM_LIPIDS"
rackCode <- "Rack Order (Column)"
plateCode <- "MTP 96"
platePos <- i@platePosition
if (i@row > 0){
sampleLocation <- RCToNum(i@row, i@column)
} else if (i@row == -1) {
sampleLocation <- "20001"
} else {
sampleLocation <- NA
}
rlist[[j]] <- data.frame("% header=SampleName" = paste0(i@sampleID, "_", j),
"SampleId" = paste0(i@sampleID, "_", j),
"RackCode" = rackCode,
"Rackpos" = rackPos,
"PlateCode" = plateCode,
"SmplInjVol" = smplInjVol,
"AcqMethod" = acqMethod,
"PlatePos" = platePos,
"VialPos" = sampleLocation,
"OutputFile" = i@runName,
"Type" = i@sampleType,
check.names = FALSE)
} else if (options$assay == "MS_EICOS") {
rackPos <- 1
smplInjVol <- 5
acqMethod <- "Eicosanoids_Quantitation-2021"
rackCode <- "Rack Order (Column)"
plateCode <- "MTP 96"
platePos <- i@platePosition
if (i@row > 0){
sampleLocation <- RCToNum(i@row, i@column)
} else {
sampleLocation <- 20001
}
rlist[[j]] <- data.frame("SampleName" = paste0(i@sampleID, "_", j),
"Rack Code" = rackCode,
"Rack position" = rackPos,
"Plate Code" = plateCode,
"PlatePos" = platePos,
"VialPos" = sampleLocation,
"Acquisition Method" = acqMethod,
"Data File" = i@runName,
"Injection Volume" = smplInjVol,
check.names = FALSE)
} else if (options$assay == "MS_URPP") {
path <- paste0("D:\\lims\\", i@projectName, "\\URPP\\")
methSet <- "D:\\Methods\\URPP\\URPP VALIDATED.m"
if (i@row == 0){
col <- (i@column %% 4) + 1
sampleLocation <- paste0("V:", col)
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Sample Type" = i@sampleType,
"Calib. Level" = 0,
"Inj." = 1,
"Volume" = 2,
"Data Path" = path,
"Run Automated Processing" = "true", check.names = FALSE)
} else if (options$assay == "MS_MRMSP") {
path <- paste0("D:\\lims\\", i@projectName, "\\MRMSP\\")
methSet <- "D:\\Methods\\FIA_Methods\\200802_Hexakis_Lockmass.m"
sepMeth <- "D:\\Methods\\FIA_Methods\\201217_LC_method.m"
msMeth <- "D:\\Methods\\FIA_Methods\\201217_MRMS_POS.m"
rlist[[j]] <- data.frame("Vial" = paste0(1, ":", i@platePosition, ":", RCToNum(i@row, i@column)),
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"MS Method" = msMeth,
"Sample Type" = i@sampleType,
"Volume [µl]" = 20,
"Data Path" = path,
"Result Path" = "", check.names = FALSE)
} else if (options$assay == "MS_MRMSN") {
# path <- "D:\\Data\\AA Methods\\Amino Acid\\"
path <- paste0("D:\\lims\\", i@projectName, "\\MRMSN\\")
methSet <- "D:\\Methods\\FIA_Methods\\200802_Hexakis_Lockmass.m"
sepMeth <- "D:\\Methods\\FIA_Methods\\201217_LC_method.m"
msMeth <- "D:\\Methods\\FIA_Methods\\201217_MRMS_NEG.m"
rlist[[j]] <- data.frame("Vial" = paste0(1, ":", i@platePosition, ":", RCToNum(i@row, i@column)),
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"MS Method" = msMeth,
"Sample Type" = i@sampleType,
"Volume [µl]" = 20,
"Data Path" = path,
"Result Path" = "", check.names = FALSE)
} else if (options$assay == "TIMS_LIPIDS_N") {
path <- paste0("D:\\lims\\", i@projectName, "\\TIMS_LIPIDS_N\\")
methSet <- ""
sepMeth <- "D:\\Methods\\CORTECS\ T3\ Lipidomics\\2020\ 0921_CORTECS\ T3_A2B2_Lipidomics_400uLmin_15min_PLNO_v1.m"
msMeth <- "D:\\Methods\\CRC-lipid_CSH_C18\\2020 0831-4D-Lipidomics_ANPC_v1.m"
procMeth <- "D:\\Data\\NaFA\ pos\ recal\ readout.m"
injMeth <- "Standard"
if (i@platePosition == 0){
sampleLocation <- paste0("V:", i@row)
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"Injection Method" = injMeth,
"MS Method" = msMeth,
"Processing Method" = procMeth,
"Sample Type" = i@sampleType,
"Inj." = 1,
"Volume [µl]" = 7.5,
"Data Path" = path,
"Run Automated Processing" = "TRUE", check.names = FALSE)
} else if (options$assay == "TIMS_LIPIDS_P") {
path <- paste0("D:\\lims\\", i@projectName, "\\TIMS_LIPIDS_P\\")
methSet <- ""
sepMeth <- "D:\\Methods\\CORTECS\ T3\ Lipidomics\\2020\ 0921_CORTECS\ T3_A2B2_Lipidomics_400uLmin_15min_PLNO_v1.m"
msMeth <- "D:\\Methods\\CRC-lipid_CSH_C18\\2020 0831-4D-Lipidomics_ANPC_v1.m"
procMeth <- "D:\\Data\\NaFA\ pos\ recal\ readout.m"
injMeth <- "Standard"
if (i@platePosition == 0){
sampleLocation <- paste0("V:", i@row)
} else {
sampleLocation <- paste0(i@platePosition, ":", row[i@row], ",", i@column)
}
rlist[[j]] <- data.frame("Vial" = sampleLocation,
"Sample ID" = paste0(i@runName, "_", i@sampleID, "_", j),
"Method Set" = methSet,
"Separation Method" = sepMeth,
"Injection Method" = injMeth,
"MS Method" = msMeth,
"Processing Method" = procMeth,
"Sample Type" = i@sampleType,
"Inj." = 1,
"Volume [µl]" = 7.5,
"Data Path" = path,
"Run Automated Processing" = "TRUE", check.names = FALSE)
} else {
rlist[[j]] <- data.frame("_sampleID" = i@sampleID,
"_matrixID" = i@matrixID,
"_runName" = i@runName,
"_sampleType" = i@sampleType,
"_methodID" = i@methodID,
"_deviceID" = i@deviceID,
"_projectName" = i@projectName,
"_platePosition" = i@platePosition,
"row" = i@row,
"column" = i@column, check.names = FALSE)
}
df <- do.call("rbind", rlist)
}
# adding shutdown blank
if (options$assay == "MSBruker") {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
path <- "D:\\Methods\\System startup\\LC Methods\\"
methSet <- "D:\\Methods\\Amino Acid VALIDATED\\Amino acid LC method SHUTDOWN.m"
sepMeth <- "Amino acid LC method SHUTDOWN"
injMeth <- "Standard"
MSMeth <- ""
procMeth <- ""
df$`Sample ID`[last] <- paste0(i@runName, "_Blank Shutdown_", last)
df$`Separation Method`[last] <- sepMeth
} else if (options$assay == "MSWaters") {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
inletFile <- "AAA end"
df$`INLET_FILE`[last] <- inletFile
df$`FILE_TEXT`[last] <- "Blank Shutdown"
df$`TYPE`[last] <- "Blank"
df$FILE_NAME[last] <- paste0(i@runName, "_BlankShutdown_", last)
} else if (options$assay == "MS-BILE") {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
df$`File Name`[last] <- paste0(i@runName, "_BlankShutdown_", last)
} else {
last <- nrow(df)
cat(crayon::blue("request >> classRequestList >> ", last, " samples were added \n"))
}
return(df)
}
)
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