| Previous changeset 17:b6b62413936f (2018-11-09) Next changeset 19:fbcf5f621aa7 (2019-03-07) |
|
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 |
|
modified:
README.rst abims_xcms_fillPeaks.xml lib.r macros_xcms.xml test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.NAless.tsv test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv xcms_fillpeaks.r |
|
removed:
lib-xcms3.x.x.r |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 README.rst --- a/README.rst Fri Nov 09 15:18:21 2018 -0500 +++ b/README.rst Mon Feb 11 06:11:33 2019 -0500 |
| b |
| @@ -2,6 +2,12 @@ Changelog/News -------------- +**Version 3.4.3.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 + +- BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378 + **Version 3.0.0.2 - 09/11/2018** - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 abims_xcms_fillPeaks.xml --- a/abims_xcms_fillPeaks.xml Fri Nov 09 15:18:21 2018 -0500 +++ b/abims_xcms_fillPeaks.xml Mon Feb 11 06:11:33 2019 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.2"> +<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.0"> <description>Integrate areas of missing peaks</description> @@ -143,7 +143,7 @@ <has_text text="object with 4 samples" /> <has_text text="Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)" /> <has_text text="Mass range: 200.1-600 m/z" /> - <has_text text="Peaks: 15230 (about 3808 per sample)" /> + <has_text text="Peaks: 15218 (about 3804 per sample)" /> <has_text text="Peak Groups: 6332" /> <has_text text="Sample classes: KO, WT" /> </assert_stdout> @@ -230,6 +230,13 @@ Changelog/News -------------- +**Version 3.4.3.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 + +- BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378 + + **Version 3.0.0.2 - 09/11/2018** - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 lib-xcms3.x.x.r --- a/lib-xcms3.x.x.r Fri Nov 09 15:18:21 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,152 +0,0 @@ - - -#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 -# https://github.com/sneumann/xcms/issues/250 -groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) { - mzfmt <- paste("%.", mzdec, "f", sep = "") - rtfmt <- paste("%.", rtdec, "f", sep = "") - - gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T", - sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "") - - if (any(dup <- duplicated(gnames))) - for (dupname in unique(gnames[dup])) { - dupidx <- which(gnames == dupname) - gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_") - } - - return (gnames) -} - -#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 -# https://github.com/sneumann/xcms/issues/247 -.concatenate_XCMSnExp <- function(...) { - x <- list(...) - if (length(x) == 0) - return(NULL) - if (length(x) == 1) - return(x[[1]]) - ## Check that all are XCMSnExp objects. - if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp"))))) - stop("All passed objects should be 'XCMSnExp' objects") - new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp") - ## If any of the XCMSnExp has alignment results or detected features drop - ## them! - x <- lapply(x, function(z) { - if (hasAdjustedRtime(z)) { - z <- dropAdjustedRtime(z) - warning("Adjusted retention times found, had to drop them.") - } - if (hasFeatures(z)) { - z <- dropFeatureDefinitions(z) - warning("Feature definitions found, had to drop them.") - } - z - }) - ## Combine peaks - fls <- lapply(x, fileNames) - startidx <- cumsum(lengths(fls)) - pks <- lapply(x, chromPeaks) - procH <- lapply(x, processHistory) - for (i in 2:length(fls)) { - pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1] - procH[[i]] <- lapply(procH[[i]], function(z) { - z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1]) - z - }) - } - pks <- do.call(rbind, pks) - new_x@.processHistory <- unlist(procH) - chromPeaks(new_x) <- pks - if (validObject(new_x)) - new_x -} - -#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 -# https://github.com/sneumann/xcms/issues/247 -.concatenate_OnDiskMSnExp <- function(...) { - x <- list(...) - if (length(x) == 0) - return(NULL) - if (length(x) == 1) - return(x[[1]]) - ## Check that all are XCMSnExp objects. - if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp"))))) - stop("All passed objects should be 'OnDiskMSnExp' objects") - ## Check processingQueue - procQ <- lapply(x, function(z) z@spectraProcessingQueue) - new_procQ <- procQ[[1]] - is_ok <- unlist(lapply(procQ, function(z) - !is.character(all.equal(new_procQ, z)) - )) - if (any(!is_ok)) { - warning("Processing queues from the submitted objects differ! ", - "Dropping the processing queue.") - new_procQ <- list() - } - ## processingData - fls <- lapply(x, function(z) z@processingData@files) - startidx <- cumsum(lengths(fls)) - ## featureData - featd <- lapply(x, fData) - ## Have to update the file index and the spectrum names. - for (i in 2:length(featd)) { - featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1] - rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames( - fileIds = featd[[i]]$fileIdx, - spectrumIds = featd[[i]]$spIdx, - nSpectra = nrow(featd[[i]]), - nFiles = length(unlist(fls)) - ) - } - featd <- do.call(rbind, featd) - featd$spectrum <- 1:nrow(featd) - ## experimentData - expdata <- lapply(x, function(z) { - ed <- z@experimentData - data.frame(instrumentManufacturer = ed@instrumentManufacturer, - instrumentModel = ed@instrumentModel, - ionSource = ed@ionSource, - analyser = ed@analyser, - detectorType = ed@detectorType, - stringsAsFactors = FALSE) - }) - expdata <- do.call(rbind, expdata) - expdata <- new("MIAPE", - instrumentManufacturer = expdata$instrumentManufacturer, - instrumentModel = expdata$instrumentModel, - ionSource = expdata$ionSource, - analyser = expdata$analyser, - detectorType = expdata$detectorType) - - ## protocolData - protodata <- lapply(x, function(z) z@protocolData) - if (any(unlist(lapply(protodata, nrow)) > 0)) - warning("Found non-empty protocol data, but merging protocol data is", - " currently not supported. Skipped.") - ## phenoData - pdata <- do.call(rbind, lapply(x, pData)) - res <- new( - "OnDiskMSnExp", - phenoData = new("NAnnotatedDataFrame", data = pdata), - featureData = new("AnnotatedDataFrame", featd), - processingData = new("MSnProcess", - processing = paste0("Concatenated [", date(), "]"), - files = unlist(fls), smoothed = NA), - experimentData = expdata, - spectraProcessingQueue = new_procQ) - if (validObject(res)) - res -} - -#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 -# https://github.com/sneumann/xcms/issues/247 -c.XCMSnExp <- function(...) { - .concatenate_XCMSnExp(...) -} - -#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 -# https://github.com/sneumann/xcms/issues/247 -c.MSnbase <- function(...) { - .concatenate_OnDiskMSnExp(...) -} |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 lib.r --- a/lib.r Fri Nov 09 15:18:21 2018 -0500 +++ b/lib.r Mon Feb 11 06:11:33 2019 -0500 |
| [ |
| @@ -144,7 +144,7 @@ #@author G. Le Corguille # Draw the plotChromPeakDensity 3 per page in a pdf file -getPlotChromPeakDensity <- function(xdata, mzdigit=4) { +getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) { pdf(file="plotChromPeakDensity.pdf", width=16, height=12) par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) @@ -156,7 +156,7 @@ for (i in 1:nrow(featureDefinitions(xdata))) { mzmin = featureDefinitions(xdata)[i,]$mzmin mzmax = featureDefinitions(xdata)[i,]$mzmax - plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) + plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) } @@ -189,10 +189,10 @@ getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { dataMatrix <- featureValues(xdata, method="medret", value=intval) colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix))) - dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix) + dataMatrix = cbind(name=groupnames(xdata), dataMatrix) variableMetadata <- featureDefinitions(xdata) colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" - variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) + variableMetadata = data.frame(name=groupnames(xdata), variableMetadata) variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 macros_xcms.xml --- a/macros_xcms.xml Fri Nov 09 15:18:21 2018 -0500 +++ b/macros_xcms.xml Mon Feb 11 06:11:33 2019 -0500 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">3.0.0</token> + <token name="@WRAPPER_VERSION@">3.4.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement> |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.NAless.tsv --- a/test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.NAless.tsv Fri Nov 09 15:18:21 2018 -0500 +++ b/test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.NAless.tsv Mon Feb 11 06:11:33 2019 -0500 |
| b |
| @@ -1047,7 +1047,7 @@ M283T4083 0 3774.77999999991 1654.73494406846 0 M283T3251 0 3469.58406459569 8415.50356074057 10826.6700000004 M283T3955 5410.20499999987 0 0 0 -M283T2530 0 0 1235.47655348411 13030.0896000001 +M283T2530 0 0 0 13030.0896000001 M283T3405 4598.76849380127 0 2384.91932829519 8454.79450000011 M283T3566 5955.89378850175 0 15354.2150000005 0 M283T3651 502256.835999998 548089.947151518 186114.495 148897.230000002 @@ -2184,7 +2184,7 @@ M365T3470 0 12244.5599999994 0 0 M365T3380 125504.867319148 187836.038181818 136522.528312009 451114.115692309 M365T4119 0 0 2854.5600000001 14340.095 -M365T2530 0 5286.48155205076 499.850080541356 6649.68500000023 +M365T2530 0 5286.48155205076 0 6649.68500000023 M365T3163 1430.34448023412 0 2041.95352711019 4034.57000000014 M365T3317 0 0 0 2680.84499999994 M365T3920 2353.60959999998 0 0 2896.81499999993 @@ -2711,7 +2711,7 @@ M404T3390 4356.96000000001 0 0 0 M404T3825 0 0 754.329999999982 0 M404T4048_1 0 1125.23499999997 0 0 -M404T2532 956.484000000008 0 214.429323162429 1812.03840000002 +M404T2532 956.484000000008 0 0 1812.03840000002 M404T3417 1365.82794954892 5386.72999999993 4155.18275950413 0 M404T4125 0 2402.12150000005 0 1541.52500000005 M404T3582 3654.41126757585 3860.67251703412 0 7348.45733333307 @@ -3678,7 +3678,7 @@ M464T3600 41973.3000000015 0 0 17959.2901555689 M464T4077 1227.21095571209 961.613246886456 5192.66999999993 1295.47964463912 M464T4194 2840.37947368416 850.484245275946 1244.70144353997 127.840484397196 -M464T2512 32103.2703333337 0 18125.8130483737 914.664000000011 +M464T2512 32103.2703333337 0 0 914.664000000011 M464T3848 17649.05403687 636509.56111111 9797.90899556107 89520.0161954499 M464T4127 344.420392126876 1433.04938568156 2796.47630000006 0 M464T2856 0 10645.1299999999 0 0 @@ -4082,7 +4082,7 @@ M489T2782 0 28800.8443076924 0 0 M489T3732 10893.4295384616 0 0 17102.0635000002 M489T3522 5319.43499999999 0 0 0 -M489T2519 1193.31250000004 0 10782.9909565296 2123.70500000007 +M489T2519 1193.31250000004 0 0 2123.70500000007 M489T3826 4623.00999999999 8442.86768747573 2151.60000000002 6137.92999999992 M489T4005 0 10309.8324705882 0 796.387722177874 M489T2595 6685.09312500002 7008.07000000002 2556.42750000001 1206.028125 @@ -4111,7 +4111,7 @@ M490T4083 1987.54999999995 0 4251.65216666652 0 M490T3024 0 0 10083.2949999998 5192.67000000018 M490T3726 11750.0199999997 0 0 0 -M490T2516 794.237499999982 0 10265.4126248753 1237.91499999997 +M490T2516 794.237499999982 0 0 1237.91499999997 M490T3511 17330.8100000006 0 13360.2659094189 0 M490T2864 0 0 7267.86000000025 2098.05196977584 M490T3806 0 0 1406.75520000001 0 @@ -4166,7 +4166,7 @@ M494T4053 0 2591.30880000002 0 0 M494T2719 0 0 0 2078.32000000007 M494T2924 0 438131.487214283 124509.849882354 0 -M494T2517 9043.69046153848 0 5008.54162654266 0 +M494T2517 9043.69046153848 0 0 0 M494T3422 1743811.96666667 1402805.175625 1595601.80785185 1773860.63070967 M494T3975 3786.27998875718 6116.02000000021 1062.18159989944 0 M494T3316 38203.8409999987 0 10507.6319999995 0 @@ -4247,7 +4247,7 @@ M499T2995 5774.84999999987 2174.98976982151 4028.29689238889 0 M499T2916 4687.17499999989 0 6498.61440000006 0 M499T3907 1265.07173716384 694.997685924502 66998.7413333334 5608.9600000002 -M499T2528 4979.19360000004 295.581319113489 0 3338.14500000012 +M499T2528 4979.19360000004 0 0 3338.14500000012 M499T3314 8783.71373606924 8266.51037749058 34282.8900000012 28931.4089999995 M499T3466 0 0 16327.6449999996 8598.57599999958 M499T4104 18625.8861250002 5178.63176065068 3333.21253115967 1446.00414158679 @@ -4384,7 +4384,7 @@ M508T3106 16326.5292423485 19052.3099999996 0 0 M508T3914 12178.0157979247 7182.11171278985 4170.58073027056 23083.9296000002 M508T4157 1875.87642341812 2220.29516038817 2690.2349999999 0 -M508T2524 3140.95500000011 2790.81607842822 4551.05002789033 569.26875000002 +M508T2524 3140.95500000011 0 0 569.26875000002 M508T4208 0 198.634842922925 1023.50999999999 0 M508T4384 938.99999999997 0 1167.43261538462 2306.81000000003 M509T3312 0 0 4760.73000000017 0 @@ -5374,7 +5374,7 @@ M558T3253 14643.7049999997 18559.4175000003 104855.449920001 41784.6459564385 M558T3711 179141.31037037 153854.257224999 1018.81500000004 118796.497722224 M558T3385 24108.476880972 30663.7071409355 19544.2668243011 182655.888800001 -M558T2519 772.953500000006 0 2141.23074708624 6267.82500000005 +M558T2519 772.953500000006 0 0 6267.82500000005 M558T3457 7743.6199999999 3000.66578009844 5407.15583885032 0 M558T4135 1580.01091242207 2945.33000000004 0 1099.74520074675 M558T2913 12901.321208686 38788.9387450146 3067.49688677633 44076.7426315788 @@ -5679,7 +5679,7 @@ M572T3167 0 0 0 1630.52160000001 M572T3340 2351.89439999988 0 1640.11999999996 0 M572T3509 19290.6343636363 2737.02317960891 0 9953.39999999993 -M572T2526 4225.49999999997 563.494442575422 0 0 +M572T2526 4225.49999999997 0 0 0 M572T2991 4217.13599999979 0 3715.89882043004 0 M572T3675 229581.565411765 11585.6949999998 6045.59499999986 1394727.71207408 M572T3758 0 2389.00001112486 1356.85500000005 3971.96999999997 @@ -5970,7 +5970,7 @@ M584T3346 147221.1063 15076.8480000001 41578.9200000002 60191.1069 M584T3239 146967.584633334 7029.9799999999 29707.8140549233 7026.17623936235 M584T3846 0 0 91884.9635833327 5422.23000000009 -M584T2532 0 2108.2768117336 Inf 3373.70880000003 +M584T2532 0 2108.2768117336 508.111776017645 3373.70880000003 M584T3524 0 3001.33253452299 4907.83999999999 0 M584T2580 518.338746330249 1871.50080000002 8093.60533333324 704.409065525723 M584T3952 15268.3957122969 6994.65600000006 6136.520295829 0 @@ -5991,7 +5991,7 @@ M585T3491 0 0 0 8172.43000000028 M585T2891 0 0 8340.68857142871 533.675426343696 M585T3409 2336.54499999995 0 0 0 -M585T2527 998.551333333313 Inf 0 7250.28861538447 +M585T2527 998.551333333313 217.104186652763 0 7250.28861538447 M585T2684 0 0 3201.98999999996 0 M585T3706 41964.3584000009 411756.431999999 27549.1498227521 74944.2896250004 M585T3493 15188.5129210785 14701.6091666669 2221.6812636937 16036.5549999998 |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv --- a/test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv Fri Nov 09 15:18:21 2018 -0500 +++ b/test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv Mon Feb 11 06:11:33 2019 -0500 |
| b |
| b'@@ -1,30 +1,30 @@\n name\tnamecustom\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tKO\tWT\tpeakidx\n M200T3488\tM200.2T3487.9\t200.199996948242\t200.199996948242\t200.199996948242\t3487.93057473838\t3487.93057473838\t3487.93057473838\t1\t1\t0\t1089,10810\n M200T3544\tM200.2T3544\t200.199996948242\t200.199996948242\t200.199996948242\t3543.97068061107\t3543.97068061107\t3543.97068061107\t1\t0\t1\t5859\n-M200T3882\tM200.2T3881.9\t200.199996948242\t200.199996948242\t200.199996948242\t3881.90389692078\t3881.90389692078\t3881.90389692078\t1\t1\t0\t1677,10811,12248\n+M200T3882\tM200.2T3881.9\t200.199996948242\t200.199996948242\t200.199996948242\t3881.90389692078\t3881.90389692078\t3881.90389692078\t1\t1\t0\t1677,10811,12245\n M200T3822\tM200.3T3822.3\t200.300003051758\t200.300003051758\t200.300003051758\t3822.28128580992\t3822.28128580992\t3822.28128580992\t1\t0\t1\t6249\n M200T3184\tM200.2T3184.4\t200.199996948242\t200.199996948242\t200.199996948242\t3184.37136447847\t3184.37136447847\t3184.37136447847\t1\t1\t0\t3054\n-M200T2867\tM200.1T2866.7\t200.100006103516\t200.100006103516\t200.100006103516\t2866.7414142519\t2866.7414142519\t2866.7414142519\t1\t1\t0\t2697,9252,12249,13693\n-M200T3978\tM200.3T3978.3\t200.300003051758\t200.300003051758\t200.300003051758\t3978.28977826224\t3978.28977826224\t3978.28977826224\t1\t0\t1\t8804,9253,12250\n-M200T3681\tM200.2T3680.7\t200.199996948242\t200.199996948242\t200.199996948242\t3680.7462381127\t3680.7462381127\t3680.7462381127\t1\t0\t1\t6014,10812,13694\n+M200T2867\tM200.1T2866.7\t200.100006103516\t200.100006103516\t200.100006103516\t2866.7414142519\t2866.7414142519\t2866.7414142519\t1\t1\t0\t2697,9252,12246,13681\n+M200T3978\tM200.3T3978.3\t200.300003051758\t200.300003051758\t200.300003051758\t3978.28977826224\t3978.28977826224\t3978.28977826224\t1\t0\t1\t8804,9253,12247\n+M200T3681\tM200.2T3680.7\t200.199996948242\t200.199996948242\t200.199996948242\t3680.7462381127\t3680.7462381127\t3680.7462381127\t1\t0\t1\t6014,10812,13682\n M201T3788\tM200.8T3787.9\t200.800003051758\t200.800003051758\t200.800003051758\t3787.9288861147\t3787.9288861147\t3787.9288861147\t1\t0\t1\t6185\n-M201T3536\tM200.8T3536.3\t200.800003051758\t200.800003051758\t200.800003051758\t3536.32508690196\t3536.32508690196\t3536.32508690196\t1\t1\t0\t3594,13695\n-M201T4052\tM200.8T4052.2\t200.800003051758\t200.800003051758\t200.800003051758\t4052.17447695121\t4052.17447695121\t4052.17447695121\t1\t0\t1\t6585,9254,10813,13696\n-M201T3276\tM200.9T3275.7\t200.900009155273\t200.900009155273\t200.900009155273\t3275.65396470411\t3275.65396470411\t3275.65396470411\t1\t0\t1\t5484,10814,13697\n-M201T3630\tM200.9T3630\t200.900009155273\t200.900009155273\t200.900009155273\t3630.01725751236\t3630.01725751236\t3630.01725751236\t1\t0\t1\t8310,12251\n+M201T3536\tM200.8T3536.3\t200.800003051758\t200.800003051758\t200.800003051758\t3536.32508690196\t3536.32508690196\t3536.32508690196\t1\t1\t0\t3594,13683\n+M201T4052\tM200.8T4052.2\t200.800003051758\t200.800003051758\t200.800003051758\t4052.17447695121\t4052.17447695121\t4052.17447695121\t1\t0\t1\t6585,9254,10813,13684\n+M201T3276\tM200.9T3275.7\t200.900009155273\t200.900009155273\t200.900009155273\t3275.65396470411\t3275.65396470411\t3275.65396470411\t1\t0\t1\t5484,10814,13685\n+M201T3630\tM200.9T3630\t200.900009155273\t200.900009155273\t200.900009155273\t3630.01725751236\t3630.01725751236\t3630.01725751236\t1\t0\t1\t8310,12248\n M201T2590\tM200.9T2590.4\t200.900009155273\t200.900009155273\t200.900009155273\t2590.41928114403\t2590.41928114403\t2590.41928114403\t1\t1\t0\t2311\n M201T3985\tM201.2T3984.7\t201.199996948242\t201.199996948242\t201.199996948242\t3984.68436009228\t3984.68436009228\t3984.68436009228\t1\t0\t1\t6528\n-M201T3138\tM201.1T3138.3\t201.100006103516\t201.100006103516\t201.100006103516\t3138.33722162086\t3138.33722162086\t3138.33722162086\t1\t1\t0\t3007,9255,12252,13698\n+M201T3138\tM201.1T3138.3\t201.100006103516\t201.100006103516\t201.100006103516\t3138.33722162086\t3138.33722162086\t3138.33722162086\t1\t1\t0\t3007,9255,12249,13686\n M201T3693\tM201.2T3692.9\t201.199996948242\t201.199996948242\t201.199996948242\t3692.85206506005\t3692.85206506005\t3692.85206506005\t1\t0\t1\t6034\n M201T3511\tM201.2T3511.4\t201.199996948242\t201.199996948242\t201.199996948242\t3511.35144568473\t3511.35144568473\t3511.35144'..b'2969\t4043.74524093865\t4043.74524093865\t4066.10087588419\t3\t1\t1\t1980,6571,6597,12244,15226\n-M599T3927\tM599.3T3927.1\t599.299987792969\t599.200012207031\t599.299987792969\t3927.1105659975\t3927.1105659975\t3973.23317972754\t3\t1\t1\t4253,8717,8748,10807,13687\n+M599T2884\tM599.1T2884\t599.100036621094\t599.100036621094\t599.100036621094\t2884.0322651969\t2884.0322651969\t2884.0322651969\t1\t0\t1\t7424,10806,12240,13674\n+M599T4044\tM599.3T4043.7\t599.299987792969\t599.299987792969\t599.299987792969\t4043.74524093865\t4043.74524093865\t4066.10087588419\t3\t1\t1\t1980,6571,6597,12241,15214\n+M599T3927\tM599.3T3927.1\t599.299987792969\t599.200012207031\t599.299987792969\t3927.1105659975\t3927.1105659975\t3973.23317972754\t3\t1\t1\t4253,8717,8748,10807,13675\n M599T3455\tM599.25T3455.1\t599.25\t599.200012207031\t599.299987792969\t3455.13028638717\t3436.14286573441\t3474.11770703993\t2\t1\t1\t1028,8116\n-M599T3741\tM599.3T3740.9\t599.299987792969\t599.299987792969\t599.400024414062\t3740.91057539316\t3733.31872427639\t3748.72918614711\t3\t1\t1\t1481,6112,6133,15227\n+M599T3741\tM599.3T3740.9\t599.299987792969\t599.299987792969\t599.400024414062\t3740.91057539316\t3733.31872427639\t3748.72918614711\t3\t1\t1\t1481,6112,6133,15215\n M599T4124\tM599.35T4123.8\t599.350006103516\t599.299987792969\t599.400024414062\t4123.8352786937\t4122.9412474863\t4124.72930990111\t2\t1\t1\t4466,9058\n-M599T3815\tM599.4T3815.4\t599.400024414062\t599.400024414062\t599.400024414062\t3815.41745314142\t3815.41745314142\t3815.41745314142\t1\t1\t0\t1552,12245,13688,15228\n-M599T2837\tM599.4T2837.3\t599.400024414062\t599.400024414062\t599.400024414062\t2837.32876796317\t2837.32876796317\t2837.32876796317\t1\t1\t0\t2616,10808,13689\n+M599T3815\tM599.4T3815.4\t599.400024414062\t599.400024414062\t599.400024414062\t3815.41745314142\t3815.41745314142\t3815.41745314142\t1\t1\t0\t1552,12242,13676,15216\n+M599T2837\tM599.4T2837.3\t599.400024414062\t599.400024414062\t599.400024414062\t2837.32876796317\t2837.32876796317\t2837.32876796317\t1\t1\t0\t2616,10808,13677\n M599T2984\tM599.45T2984.4\t599.450012207031\t599.400024414062\t599.5\t2984.36512439418\t2969.43152576515\t2999.29872302321\t2\t1\t1\t2885,7528\n M600T3611\tM599.5T3611.3\t599.5\t599.5\t599.5\t3611.27081973131\t3611.27081973131\t3611.27081973131\t1\t0\t1\t8294\n M600T2728\tM599.5T2728.4\t599.5\t599.5\t599.5\t2728.42534632355\t2728.42534632355\t2728.42534632355\t1\t0\t1\t7235\n-M600T3412\tM599.5T3412.5\t599.5\t599.5\t599.5\t3412.49713875326\t3412.49713875326\t3412.49713875326\t1\t1\t0\t999,12246\n+M600T3412\tM599.5T3412.5\t599.5\t599.5\t599.5\t3412.49713875326\t3412.49713875326\t3412.49713875326\t1\t1\t0\t999,12243\n M600T2595\tM599.85T2594.7\t599.850006103516\t599.799987792969\t599.900024414062\t2594.74502674603\t2557.12926551055\t2601.08568100398\t4\t2\t2\t75,2316,4673,7054\n M600T2782\tM599.9T2782.4\t599.900024414062\t599.900024414062\t599.900024414062\t2782.43037673\t2782.43037673\t2782.43037673\t1\t0\t1\t7290\n M600T3443\tM600T3443.3\t600\t600\t600\t3443.33609503605\t3428.56063072458\t3458.11155934752\t2\t2\t0\t1049,3394\n-M600T2847\tM600T2846.8\t600\t600\t600\t2846.75746804785\t2846.75746804785\t2846.75746804785\t1\t0\t1\t7388,13690\n-M600T2963\tM600T2963.2\t600\t600\t600\t2963.21691026891\t2963.21691026891\t2963.21691026891\t1\t1\t0\t455,13691,15229\n-M600T3070\tM600T3070\t600\t600\t600\t3069.97823403078\t3069.97823403078\t3069.97823403078\t1\t0\t1\t7609,10809,13692\n-M600T3353\tM600T3352.9\t600\t600\t600\t3352.93056227251\t3352.93056227251\t3352.93056227251\t1\t1\t0\t903,15230\n-M600T3212\tM600T3212.3\t600\t600\t600\t3212.26402887262\t3212.26402887262\t3212.26402887262\t1\t1\t0\t705,12247\n+M600T2847\tM600T2846.8\t600\t600\t600\t2846.75746804785\t2846.75746804785\t2846.75746804785\t1\t0\t1\t7388,13678\n+M600T2963\tM600T2963.2\t600\t600\t600\t2963.21691026891\t2963.21691026891\t2963.21691026891\t1\t1\t0\t455,13679,15217\n+M600T3070\tM600T3070\t600\t600\t600\t3069.97823403078\t3069.97823403078\t3069.97823403078\t1\t0\t1\t7609,10809,13680\n+M600T3353\tM600T3352.9\t600\t600\t600\t3352.93056227251\t3352.93056227251\t3352.93056227251\t1\t1\t0\t903,15218\n+M600T3212\tM600T3212.3\t600\t600\t600\t3212.26402887262\t3212.26402887262\t3212.26402887262\t1\t1\t0\t705,12244\n M600T2573\tM600T2573.2\t600\t600\t600\t2573.20528114403\t2573.20528114403\t2573.20528114403\t1\t1\t0\t2295\n' |
| b |
| diff -r b6b62413936f -r 27fbe73c4279 xcms_fillpeaks.r --- a/xcms_fillpeaks.r Fri Nov 09 15:18:21 2018 -0500 +++ b/xcms_fillpeaks.r Mon Feb 11 06:11:33 2019 -0500 |
| [ |
| @@ -12,7 +12,6 @@ #Import the different functions source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } source_local("lib.r") -source_local("lib-xcms3.x.x.r") pkgs <- c("xcms","batch") loadAndDisplayPackages(pkgs) @@ -67,7 +66,6 @@ cat("\n\n") - # ----- MAIN PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") @@ -80,6 +78,10 @@ fillChromPeaksParam <- do.call(paste0(method,"Param"), args) print(fillChromPeaksParam) + +# back compatibility between xcms-3.0.0 and xcms-3.5.2 +xdata <- updateObject(xdata) + xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam) if (exists("intval")) { |