Hi,
which peak exactly are you missing ? As you see below, I can happily find
the M184T407.
Yours,
Steffen
sneumann@acryl:/tmp/maialba$ R
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(xcms)
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
Loading required package: ProtGenerics
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MSnbase
Loading required package: BiocParallel
This is MSnbase version 2.1.10
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: ‘MSnbase’
The following object is masked from ‘package:stats’:
smooth
The following object is masked from ‘package:base’:
trimws
This is xcms version 1.51.9
>
> file <- "acq1.mzXML"
>
> xs <- xcmsSet(file, method="centWave", ppm=10, peakwidth=c(3,25), snthresh=2, mzCenterFun="wMean", integrate=2, fitgauss=F, scanrange=NULL, noise=0, sleep=0, verbose.columns=F)
DEBUG: using original centWave.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 31566 regions of interest ... OK: 12594 found.
>
> peaks(xs)[peaks(xs)[,"mz"] < 185 & peaks(xs)[,"mz"] > 184 & peaks(xs)[,"rt"] < 450 & peaks(xs)[,"rt"] > 350, ]
mz mzmin mzmax rt rtmin rtmax into intb
[1,] 184.0751 184.0749 184.0752 407.033 400.336 412.055 32211658.9 32192175.1
[2,] 184.0748 184.0746 184.0750 448.890 442.190 456.424 45293500.1 45270113.3
[3,] 184.0743 184.0742 184.0745 385.269 376.898 390.291 7070136.5 7048055.0
[4,] 184.0743 184.0742 184.0745 371.038 366.016 376.898 2287296.5 2269111.5
[5,] 184.0746 184.0745 184.0747 437.168 424.612 442.190 35453580.9 35425005.4
[6,] 184.0745 184.0743 184.0746 416.241 412.055 424.612 19979393.7 19958609.4
[7,] 184.0743 184.0742 184.0744 361.830 356.808 366.016 793141.5 777554.1
[8,] 184.0743 184.0742 184.0745 395.314 390.291 400.336 4780042.9 4763156.6
[9,] 184.0744 184.0743 184.0746 429.634 424.612 431.308 9079473.6 9067784.3
maxo sn sample
[1,] 4220260.0 5793 1
[2,] 3970454.8 5450 1
[3,] 1122035.1 1539 1
[4,] 421025.2 576 1
[5,] 3052630.8 4190 1
[6,] 2557234.2 3510 1
[7,] 107556.0 146 1
[8,] 691897.0 948 1
[9,] 1943207.9 2666 1
>
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] xcms_1.51.9 MSnbase_2.1.10 BiocParallel_1.9.4
[4] Biobase_2.30.0 ProtGenerics_1.7.0 BiocGenerics_0.16.1
[7] mzR_2.9.10 Rcpp_0.12.8
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 BiocInstaller_1.20.3 plyr_1.8.4
[4] iterators_1.0.8 tools_3.2.3 zlibbioc_1.16.0
[7] MALDIquant_1.16 digest_0.6.11 tibble_1.2
[10] preprocessCore_1.32.0 gtable_0.2.0 lattice_0.20-33
[13] Matrix_1.2-3 foreach_1.4.3 stringr_1.1.0
[16] S4Vectors_0.8.11 IRanges_2.4.8 multtest_2.26.0
[19] stats4_3.2.3 grid_3.2.3 impute_1.44.0
[22] survival_2.40-1 XML_3.98-1.5 RANN_2.5
[25] limma_3.26.9 ggplot2_2.2.1 reshape2_1.4.2
[28] magrittr_1.5 MASS_7.3-45 splines_3.2.3
[31] scales_0.4.1 pcaMethods_1.60.0 codetools_0.2-14
[34] MassSpecWavelet_1.36.0 assertthat_0.1 mzID_1.13.0
[37] colorspace_1.3-2 stringi_1.1.2 affy_1.48.0
[40] lazyeval_0.2.0 munsell_0.4.3 doParallel_1.0.10
[43] vsn_3.38.0 affyio_1.40.0