Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Removes low intensity peaksDescriptionThis method sets low intensity peaks from individual spectra
( If the spectrum is in profile mode, ranges of successive non-0 peaks
<= Note that the number of peaks is not changed; the peaks below the
threshold are set to 0 and the object is not cleanded out (see
Methods
Author(s)Laurent Gatto <lg390@cam.ac.uk> See Also
Examples
int <- c(2,0,0,0,1,5,1,0,0,1,3,1,0,0,1,4,2,1)
sp1 <- new("Spectrum2",
intensity=int,
mz=1:length(int))
sp2 <- removePeaks(sp1) ## no peaks are removed here
## as min intensity is 1 and
## no peak has a max int <= 1
sp3 <- removePeaks(sp1,3)
intensity(sp1)
intensity(sp2)
intensity(sp3)
peaksCount(sp1) == peaksCount(sp2)
peaksCount(sp3) <= peaksCount(sp1)
data(itraqdata)
itraqdata2 <- removePeaks(itraqdata, t = 2.5e5)
table(unlist(intensity(itraqdata)) == 0)
table(unlist(intensity(itraqdata2)) == 0)
processingData(itraqdata2)
## difference between centroided and profile peaks
int <- c(104, 57, 32, 33, 118, 76, 38, 39, 52, 140, 52, 88, 394, 71,
408, 94, 2032)
sp <- new("Spectrum2",
intensity = int,
centroided = FALSE,
mz = seq_len(length(int)))
## unchanged, as ranges of peaks <= 500 considered
intensity(removePeaks(sp, 500))
centroided(sp) <- TRUE
## different!
intensity(removePeaks(sp, 500))
Results
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> library(MSnbase)
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
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: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MSnbase/removePeaks-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: removePeaks-methods
> ### Title: Removes low intensity peaks
> ### Aliases: removePeaks-methods removePeaks
> ### Keywords: methods
>
> ### ** Examples
>
> int <- c(2,0,0,0,1,5,1,0,0,1,3,1,0,0,1,4,2,1)
> sp1 <- new("Spectrum2",
+ intensity=int,
+ mz=1:length(int))
> sp2 <- removePeaks(sp1) ## no peaks are removed here
> ## as min intensity is 1 and
> ## no peak has a max int <= 1
> sp3 <- removePeaks(sp1,3)
> intensity(sp1)
[1] 2 0 0 0 1 5 1 0 0 1 3 1 0 0 1 4 2 1
> intensity(sp2)
[1] 2 0 0 0 1 5 1 0 0 1 3 1 0 0 1 4 2 1
> intensity(sp3)
[1] 0 0 0 0 1 5 1 0 0 0 0 0 0 0 1 4 2 1
>
> peaksCount(sp1) == peaksCount(sp2)
[1] TRUE
> peaksCount(sp3) <= peaksCount(sp1)
[1] TRUE
>
> data(itraqdata)
> itraqdata2 <- removePeaks(itraqdata, t = 2.5e5)
| | | 0% | |= | 2% | |=== | 4% | |==== | 5% | |===== | 7% | |====== | 9% | |======== | 11% | |========= | 13% | |========== | 15% | |=========== | 16% | |============= | 18% | |============== | 20% | |=============== | 22% | |================= | 24% | |================== | 25% | |=================== | 27% | |==================== | 29% | |====================== | 31% | |======================= | 33% | |======================== | 35% | |========================= | 36% | |=========================== | 38% | |============================ | 40% | |============================= | 42% | |=============================== | 44% | |================================ | 45% | |================================= | 47% | |================================== | 49% | |==================================== | 51% | |===================================== | 53% | |====================================== | 55% | |======================================= | 56% | |========================================= | 58% | |========================================== | 60% | |=========================================== | 62% | |============================================= | 64% | |============================================== | 65% | |=============================================== | 67% | |================================================ | 69% | |================================================== | 71% | |=================================================== | 73% | |==================================================== | 75% | |===================================================== | 76% | |======================================================= | 78% | |======================================================== | 80% | |========================================================= | 82% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================= | 87% | |============================================================== | 89% | |================================================================ | 91% | |================================================================= | 93% | |================================================================== | 95% | |=================================================================== | 96% | |===================================================================== | 98% | |======================================================================| 100%
> table(unlist(intensity(itraqdata)) == 0)
FALSE TRUE
45628 60661
> table(unlist(intensity(itraqdata2)) == 0)
FALSE TRUE
10280 96009
> processingData(itraqdata2)
- - - Processing information - - -
Data loaded: Wed May 11 18:54:39 2011
Curves <= 250000 set to '0': Wed Jul 6 01:10:31 2016
MSnbase version: 1.1.22
>
> ## difference between centroided and profile peaks
>
> int <- c(104, 57, 32, 33, 118, 76, 38, 39, 52, 140, 52, 88, 394, 71,
+ 408, 94, 2032)
> sp <- new("Spectrum2",
+ intensity = int,
+ centroided = FALSE,
+ mz = seq_len(length(int)))
>
> ## unchanged, as ranges of peaks <= 500 considered
> intensity(removePeaks(sp, 500))
[1] 104 57 32 33 118 76 38 39 52 140 52 88 394 71 408
[16] 94 2032
>
>
> centroided(sp) <- TRUE
> ## different!
> intensity(removePeaks(sp, 500))
[1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[16] 0 2032
>
>
>
>
>
> dev.off()
null device
1
>
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and