Comments (6)
Install and test Rcode snippet
install.packages('rDotNet')
install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.35.tar.gz', repo=NULL)
library(rawDiag)
(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
S <- csReadScans(rawfile, 1:9)
S[1]
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https://CRAN.R-project.org/package=rDotNet
#R
require(rDotNet)
## initialize
.cinit(dll="/Users/cp//__checkouts/R/rawDiag/exec/fgcz_raw.dll")
rawfile <- file.path(Sys.getenv("HOME"), "Downloads/20180220_14_autoQC01.raw")
## create an object and call a method
(obj <- .cnew ("Rawfile", rawfile))
obj$check()
obj$getFirstScanNumber()
obj$IsCentroidScan(2)
(L <- obj$GetSpectrum(1, ""))
(L <- obj$GetSpectrum(2, ""))
from rawdiag.
kill -9 `ps aux | grep CLRServer| awk '{print $2}' | tail -n 1 ` && ./build_linux_fgcz_raw.bash
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from rawdiag.
Line 265 in f9d53c0
refactor readScans
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Works!
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rawDiag_0.0.35 rDotNet_0.9.1
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 purrr_0.3.2 haven_2.1.0 lattice_0.20-38 colorspace_1.4-1
[6] generics_0.0.2 testthat_2.1.1 yaml_2.2.0 blob_1.1.1 rlang_0.3.2
[11] hexbin_1.27.2 pillar_1.3.1 glue_1.3.1 DBI_1.0.0 tidyverse_1.2.1
[16] bit64_0.9-7 modelr_0.1.4 readxl_1.3.1 protViz_0.4.0 plyr_1.8.4
[21] stringr_1.4.0 munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0 rvest_0.3.2
[26] codetools_0.2-16 memoise_1.1.0 forcats_0.4.0 parallel_3.5.3 broom_0.5.1
[31] Rcpp_1.0.1 readr_1.3.1 backports_1.1.3 scales_1.0.0 jsonlite_1.6
[36] bit_1.1-14 ggplot2_3.1.0 hms_0.4.2 digest_0.6.18 stringi_1.4.3
[41] dplyr_0.8.0.1 grid_3.5.3 tools_3.5.3 magrittr_1.5 lazyeval_0.2.2
[46] tibble_2.1.1 RSQLite_2.1.1 crayon_1.3.4 tidyr_0.8.3 pkgconfig_2.0.2
[51] xml2_1.2.0 lubridate_1.7.4 assertthat_0.2.1 httr_1.4.0 rstudioapi_0.10
[56] R6_2.4.0 nlme_3.1-137 compiler_3.5.3
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Related Issues (20)
- plot.peaklist function does not allow to overwrite title and y- n xlabels
- R 4.0.2 - Error: `x` must be a vector, not a `data.frame/rawDiag` object. HOT 3
- Problems reading Meta Data from QExactive HF / HFX Instruments HOT 28
- Reading Analag Traces from RawFiles HOT 7
- Read additional Infos from Raw Files (Status Log, Tune Method) etc. HOT 10
- create unit test for `read.raw.info()`
- Cannot find dependency "Spectra" HOT 2
- .computeBestPeptideSpectrumMatch function HOT 11
- Installation of new RawFileReader files HOT 19
- Error in source(tfo) : negative length vectors are not allowed HOT 15
- replace `warning` with `message`
- Deprecation messages for read.XIC() and readScans() HOT 1
- `funs()` was deprecated in dplyr 0.8.0.
- Error in FUN(left, right) : non-numeric argument to binary operator in `PlotCycleTime` HOT 2
- issues with tempfile opening
- I am trying to run read.raw, but it returns an error HOT 1
- [Extra feature that would be nice] Using m/z / RT values for QCs rather peptides
- protViz 0.6.8 required prior to install rawDiag on R.4.0.5
- Package "mardown" and "plyr" have to be installed so the ShinyApp works
- Problems with the read.raw()
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