calculate.dNSAF: dNSAF approximate abundance calculations.
In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
View source: R/ProteinGroup-class.R
Description
Distributed normalized spectral abundance factor (dNSAF) is a
label free quantitative measure of protein abundance based on
spectral counts which are corrected for peptides shared by multiple
proteins. Original publication: Zhang Y et al., Analytical Chemistry
(2010).
Usage
1
2
calculate.dNSAF(protein.group, use.mw = FALSE, normalize = TRUE,
combine.f = mean)
Arguments
protein.group
ProteinGroup object. Its @proteinInfo
slot data.frame must contain a length column.
use.mw
Use MW to account for protein size
normalize
Normalize dSAF to dNSAF?
combine.f
How to handle proteins seen only with shared peptides?
Value
Named numeric vector of dNSAF values.
Author(s)
Florian P Breitwieser
References
Zhang Y et al., Analytical Chemistry (2010)
See Also
proteinInfo,
getProteinInfoFromUniprot,
calculate.emPAI,
ProteinGroup
Examples
1
2
3
data(ibspiked_set1)
protein.group <- proteinGroup(ibspiked_set1)
calculate.dNSAF(protein.group)
Example output
Loading required package: Biobase
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Welcome to isobar (v 1.22.0)
'openVignette("isobar")' and '?isobar' provide help on usage.
Attaching package: 'isobar'
The following object is masked from 'package:BiocGenerics':
normalize
The following object is masked from 'package:base':
paste0
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P03952 P01008
6.844970e-03 1.237619e-02
P02649 P02675
2.614245e-02 7.633672e-03
P13635 P05156
1.664752e-02 5.426350e-03
P06727 P00736
6.425768e-03 6.048130e-03
P04264 P07358
4.039796e-03 6.051101e-03
P02647 P02790
9.916718e-03 3.021848e-02
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3.326450e-03 4.048416e-03
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P06276 P08697
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P35908 P43652
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P51884 P01031
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P48740-2 P01766
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P01779
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isobar documentation built on Nov. 8, 2020, 7:48 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
View source: R/ProteinGroup-class.R
Description
Distributed normalized spectral abundance factor (dNSAF) is a label free quantitative measure of protein abundance based on spectral counts which are corrected for peptides shared by multiple proteins. Original publication: Zhang Y et al., Analytical Chemistry (2010).
Usage
1 2 | calculate.dNSAF(protein.group, use.mw = FALSE, normalize = TRUE,
combine.f = mean)
|
Arguments
protein.group |
ProteinGroup object. Its |
use.mw |
Use MW to account for protein size |
normalize |
Normalize dSAF to dNSAF? |
combine.f |
How to handle proteins seen only with shared peptides? |
Value
Named numeric vector of dNSAF values.
Author(s)
Florian P Breitwieser
References
Zhang Y et al., Analytical Chemistry (2010)
See Also
proteinInfo,
getProteinInfoFromUniprot,
calculate.emPAI,
ProteinGroup
Examples
1 2 3 | data(ibspiked_set1)
protein.group <- proteinGroup(ibspiked_set1)
calculate.dNSAF(protein.group)
|
Example output
Loading required package: Biobase
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Welcome to isobar (v 1.22.0)
'openVignette("isobar")' and '?isobar' provide help on usage.
Attaching package: 'isobar'
The following object is masked from 'package:BiocGenerics':
normalize
The following object is masked from 'package:base':
paste0
P01024 P02787
1.751377e-02 4.162841e-02
P01023 P0C0L4,P0C0L5
9.564778e-03 5.264454e-03
P00747 P02671-1,P02671-2
8.787672e-03 1.528732e-02
P03952 P01008
6.844970e-03 1.237619e-02
P02649 P02675
2.614245e-02 7.633672e-03
P13635 P05156
1.664752e-02 5.426350e-03
P06727 P00736
6.425768e-03 6.048130e-03
P04264 P07358
4.039796e-03 6.051101e-03
P02647 P02790
9.916718e-03 3.021848e-02
P00450 P09871
3.326450e-03 4.048416e-03
P10909-1,P10909-2 P02679-1,P02679-2
1.282794e-02 2.846568e-03
P05155 P00751-1
3.101666e-02 6.571250e-03
Q61147 P05543
9.667204e-03 6.877309e-03
P13645 P00738
2.078829e-03 8.105399e-02
P10643 P29622
8.158136e-04 4.831833e-03
P36955 P01011-1
3.537372e-03 5.105142e-02
P06276 P08697
1.942097e-03 4.342089e-03
P22792 O14791-1,O14791-2
2.965445e-03 2.462353e-03
P02768-1 P05546
1.465059e-02 2.274060e-03
P07357 P35527
1.000978e-03 1.655853e-03
P00740 P04003
2.721669e-03 1.151978e-03
P04004 P04217
6.258639e-03 2.917646e-03
Q9UK55 P01019
1.316602e-03 1.184031e-02
P02765 P04114
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P04196 P18428
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162648 P00734
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P51884 P01031
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P27169 Q08380
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P01871-1,P01871-2 P02746
3.088703e-03 2.310558e-03
P02748 P02750
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3.963867e-04 5.293410e-04
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1.625134e-03 9.143137e-03
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8.511521e-04 5.546217e-04
P13647 P49747
3.643413e-04 1.816990e-04
P69905 Q14624-1
1.452953e-03 7.764703e-03
A6NJ16 P01042-2
4.193481e-03 1.811701e-02
P01591 P01743
4.325351e-04 2.645119e-03
P01763 P01857
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P01861 P02654
7.940336e-04 8.285914e-04
P02743 P06396-1
4.625992e-04 1.969971e-02
P06681 P08603-1
9.145357e-05 1.361309e-03
P11597-1 P14151
2.092487e-04 8.319325e-04
P19827 P36980-1,P36980-2
1.132378e-04 5.458181e-04
Q03591 Q13098-4,Q13098-5,Q13098-6,Q13098-7
3.850499e-04 5.252527e-05
Q16610-1,Q16610-4 Q8NEZ4-1,Q8NEZ4-2,Q8NEZ4-3
6.367878e-05 1.166991e-05
Q92496 Q9C0I3-1,Q9C0I3-2
1.350529e-03 3.820727e-05
Q9UJV8-2 Q9Y6R7
1.981933e-04 1.272398e-05
O75636-1 P00338-1,P00338-2
8.855397e-03 1.035739e-04
P00748 P01042-1
1.677392e-04 2.013001e-03
P01764 P01776
1.058047e-02 1.122172e-03
P01859 P02533
2.822886e-03 6.232966e-04
P02745 P04220
1.403532e-04 2.462463e-04
P04278-1 P06331
1.112003e-03 3.768388e-03
P08571 P23083
9.169745e-05 8.817062e-04
P23142-1 P23142-4
1.497991e-03 2.139988e-04
P68871 Q04695
2.339221e-04 1.702523e-04
Q15485-1 Q6UXB8-1,Q6UXB8-2
6.591670e-04 3.713450e-05
Q9HDC9-1 P02538,P48668
4.132998e-04 6.906551e-05
P48740-2 P01766
1.844772e-04 3.857465e-03
P01779
3.018255e-03
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