ASICS - importing 1r files
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Last seen 3.0 years ago

I am trying to use ASICS for analysis of my NMR spectra.

spectra_data <- importSpectraBruker(name.dir = "C:/Spectra/NMR/Must test", sample.names = NULL, ncores = 6, ppm.grid = NULL, verbose = TRUE)

When imported, they show only 31087 points whereas all my spectra have 65536 points. I suppose it has something to do with the "ppm.grid" parameter.

It is said in the manual that is is

"Numeric vector of a unique grid (definition domain) for all spectra (in ppm). Default to NULL (in which case, the default grid of the pure library is used)."

How can I change the ppm.grid so all 65536 points will be imported?

Thanks in advance

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LCCOLLATE=ItalianItaly.1252 LCCTYPE=ItalianItaly.1252 LCMONETARY=ItalianItaly.1252 LCNUMERIC=C LCTIME=Italian_Italy.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] mdatools0.9.4 ASICS2.0.1

loaded via a namespace (and not attached): [1] Biobase2.44.0 jsonlite1.6.1 TSclust1.2.4 shiny1.4.0 assertthat0.2.1
[6] stats4
3.6.1 TSdist3.6 GenomeInfoDbData1.2.1 pillar1.4.3 lattice0.20-38
[11] quadprog1.5-8 glue1.3.1 digest0.6.23 manipulateWidget0.10.0 GenomicRanges1.36.1
[16] promises
1.1.0 XVector0.24.0 colorspace1.4-1 htmltools0.4.0 httpuv1.5.2
[21] Matrix1.2-17 plyr1.8.5 pkgconfig2.0.3 misc3d0.8-4 longitudinalData2.4.1
[26] zlibbioc
1.30.0 purrr0.3.3 xtable1.8-4 webshot0.5.2 ptw1.9-15
[31] scales1.1.0 PepsNMR1.2.1 locpol0.7-0 later1.0.0 ifultools2.0-5
[36] BiocParallel
1.18.1 dtw1.21-3 tibble2.1.3 proxy0.4-23 farver2.0.3
[41] IRanges2.18.3 ggplot23.2.1 SummarizedExperiment1.14.1 BiocGenerics0.30.0 lazyeval0.2.2
[46] magrittr
1.5 crayon1.3.4 mime0.8 MASS7.3-51.4 xts0.12-0
[51] class7.3-15 ropls1.16.0 tools3.6.1 lifecycle0.1.0 matrixStats0.55.0
[56] stringr
1.4.0 clv0.3-2.1 S4Vectors0.22.1 munsell0.5.0 cluster2.1.0
[61] DelayedArray0.10.0 wmtsa2.0-3 compiler3.6.1 GenomeInfoDb1.20.0 rlang0.4.4
[66] grid
3.6.1 RCurl1.98-1.1 nloptr1.2.1 rstudioapi0.10 htmlwidgets1.5.1
[71] miniUI0.1.1.1 crosstalk1.0.0 labeling0.3 bitops1.0-6 gtable0.3.0
[76] reshape2
1.4.3 R62.4.1 gridExtra2.3 zoo1.8-7 knitr1.27
[81] dplyr0.8.4 fastmap1.0.1 KernSmooth2.23-15 pdc1.0.3 stringi1.4.5
[86] parallel
3.6.1 Rcpp1.0.3 splus2R1.2-2 rgl0.100.30 tidyselect1.0.0
[91] xfun_0.12

asics ppm.grid • 247 views

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