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1
November 27, 2021, 12:14:14 AM
Dear Johannes I save and load the xcmsSet object: save(xset, file = "xset.RData") xset = load("xset.RData") But I think it needs type conversion after being loaded. Would you please tell me how to convert it to an xcmsSet object? I just found type.convert(), but it dose not work in this case. Thanks in advance Narges
2
November 24, 2021, 11:50:21 PM
Dear Johannes Many thanks for your quick help Bests Narges
3
November 24, 2021, 04:30:40 AM
Hi all, I am working on a metabolic dataset using XCMS pipeline. Is there a way to save the intermediate xcmsSet objects as a file which can be loaded and used later by the needed functions? e.g. loading the result of the xcmsSet() inside the group(). Thanks
4
November 12, 2021, 02:12:23 AM
Hi all, I am working on a mzML dataset. I run the following script, but all the generated csv files, almost are identical. It seems that the group() function can not group the samples (dim(xset2) == NULL). According to a suggestion, I put the files in subfolders, but xcmsSet can not find them now. I am not sure if I have get the meaning correctly. Any help? Thanks ---------------------------------------------------------------------------------------------------------------------- library(xcms) library(CAMERA) path <- "/mzML/Split/xinb3_4h" datafiles <- list.files(path, full.names=T, pattern='.mzML') xcmsSet(files=datafiles, recursive = TRUE, method="centWave", ppm=20, snthr=10, peakwidth=c(5,25), integrate=1) write.csv(xset1@peaks, "all_peaks.csv") print("all_peaks.csv generated") xset2 <- group(xset_cent20, method="density", bw=4, minfrac=0, minsamp=1, mzwid=0.007, max=100) write.csv(xset2@peaks, "grouped_peaks.csv") print("grouped_peaks.csv generated") print("Dimention of grouped_peak:") dim(xset2) xset3 <- retcor(xset2) write.csv(xset3@peaks, "retcor_peaks.csv") print("retcor_peaks.csv generated") xset4 <- group(xset3) write.csv(xset4@peaks, "regrouped_peaks.csv") print("regrouped_peaks.csv generated") xset5 <- fillPeaks(xset4, method="chrom") write.csv(xset5@peaks, "filled_peaks.csv") print("filled_peaks.csv generated") an <- xsAnnotate(xset5, sample=NA) anF <- groupFWHM(an, perfwhm = 0.6) anI <- findIsotopes(anF, mzabs=0.01) anIC <- groupCorr(anI, cor_eic_th=0.75) anFA <- findAdducts(anIC, polarity="positive") write.csv(getPeaklist(anFA), file="annotated_peaks.csv") print("annotated_peaks.csv generated") ---------------------------------------------------------------------------------------------------------------------
5
November 12, 2021, 02:11:04 AM
Hi all, I am working on a mzML dataset. I run the following script, but all the generated csv files, almost are identical. It seems that the group() function can not group the samples (dim(xset2) == NULL). According to a suggestion, I put the files in subfolders, but xcmsSet can not find them now. I am not sure if I have get the meaning correctly. Any help? Thanks ---------------------------------------------------------------------------------------------------------------------- library(xcms) library(CAMERA) path <- "/mzML/Split/xinb3_4h" datafiles <- list.files(path, full.names=T, pattern='.mzML') xcmsSet(files=datafiles, recursive = TRUE, method="centWave", ppm=20, snthr=10, peakwidth=c(5,25), integrate=1) write.csv(xset1@peaks, "all_peaks.csv") print("all_peaks.csv generated") xset2 <- group(xset_cent20, method="density", bw=4, minfrac=0, minsamp=1, mzwid=0.007, max=100) write.csv(xset2@peaks, "grouped_peaks.csv") print("grouped_peaks.csv generated") print("Dimention of grouped_peak:") dim(xset2) xset3 <- retcor(xset2) write.csv(xset3@peaks, "retcor_peaks.csv") print("retcor_peaks.csv generated") xset4 <- group(xset3) write.csv(xset4@peaks, "regrouped_peaks.csv") print("regrouped_peaks.csv generated") xset5 <- fillPeaks(xset4, method="chrom") write.csv(xset5@peaks, "filled_peaks.csv") print("filled_peaks.csv generated") an <- xsAnnotate(xset5, sample=NA) anF <- groupFWHM(an, perfwhm = 0.6) anI <- findIsotopes(anF, mzabs=0.01) anIC <- groupCorr(anI, cor_eic_th=0.75) anFA <- findAdducts(anIC, polarity="positive") write.csv(getPeaklist(anFA), file="annotated_peaks.csv") print("annotated_peaks.csv generated") ---------------------------------------------------------------------------------------------------------------------