## load R package
library(msDiaLogue)
## preprocessing
fileName <- "../inst/extdata/Toy_Spectronaut_Data.csv"
dataSet <- preprocessing(fileName,
filterNaN = TRUE, filterUnique = 2,
replaceBlank = TRUE, saveRm = TRUE)
## transformation
dataTran <- transform(dataSet, logFold = 2)
## annotation-based filtering
dataFiltAnno <- filterOutIn(dataTran, listName = "ALBU_BOVIN",
removeList = TRUE, saveRm = TRUE)
## normalization
dataNorm <- normalize(dataFiltAnno, normalizeType = "median")
## data-driven filtering
dataFilt <- filterNA(dataNorm, minProp = 0.51, by = "cond", saveRm = TRUE)
## imputation
dataImput <- impute.min_local(dataFilt)Preliminary
pullProteinPath
The function pullProteinPath() allows you to see the quantitative values associated with specific proteins at each step of processing, using either the exact match argument listname, or the text match argument regexName, or both.
This can be useful for questions such as,
- “Which of the values for my favorite protein were actually measured, vs. imputed?”
- “Why didn’t my favorite protein make it to the final list? At what step was it filtered out?”.
It can also be used to check whether the fold-change observed for a specific protein is an artifact from one of the processing steps.
Check <- pullProteinPath(
listName = c("LYSC_CHICK", "BGAL_ECOLI"),
regexName = c("BOVIN"),
by = "PG.ProteinNames",
dataSetList = list(Initial = dataSet,
Transformed = dataTran,
Normalized = dataNorm,
Imputed = dataImput))| PG.ProteinNames | PG.Genes | PG.ProteinAccession | PG.ProteinAccessions | PG.ProteinDescriptions | PG.ProteinName | R.Condition | R.Replicate | Initial | Transformed | Normalized | Imputed |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 100pmol | 1 | 111209.703 | 16.76292 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 100pmol | 2 | 111659.883 | 16.76875 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 100pmol | 3 | 105982.914 | 16.69347 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 100pmol | 4 | 104442.562 | 16.67235 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 200pmol | 1 | 109245.289 | 16.73721 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 200pmol | 2 | 113357.508 | 16.79052 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 200pmol | 3 | 114321.836 | 16.80274 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 200pmol | 4 | 116439.820 | 16.82923 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 50pmol | 1 | 117803.492 | 16.84602 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 50pmol | 2 | 110086.680 | 16.74828 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 50pmol | 3 | 105640.203 | 16.68880 | NA | NA |
| ALBU_BOVIN | ALB | CON__P02769 | CON__P02769 | Bovine serum albumin | ALBU_BOVIN | 50pmol | 4 | 110446.000 | 16.75298 | NA | NA |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 100pmol | 1 | 23840.031 | 14.54110 | 4.602821 | 4.602821 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 100pmol | 2 | 23963.307 | 14.54854 | 4.995489 | 4.995489 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 100pmol | 3 | 22957.350 | 14.48667 | 4.690354 | 4.690354 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 100pmol | 4 | 22311.297 | 14.44549 | 4.629191 | 4.629191 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 200pmol | 1 | 41234.672 | 15.33157 | 6.005343 | 6.005343 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 200pmol | 2 | 42899.434 | 15.38867 | 5.748865 | 5.748865 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 200pmol | 3 | 42904.945 | 15.38886 | 6.070587 | 6.070587 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 200pmol | 4 | 43279.844 | 15.40141 | 6.343191 | 6.343191 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 50pmol | 1 | 14728.673 | 13.84634 | 4.671661 | 4.671661 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 50pmol | 2 | 14736.710 | 13.84713 | 4.912229 | 4.912229 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 50pmol | 3 | 14160.203 | 13.78955 | 4.927047 | 4.927047 |
| BGAL_ECOLI | lacZ | P00722 | P00722 | Beta-galactosidase | BGAL_ECOLI | 50pmol | 4 | 14758.731 | 13.84928 | 4.637064 | 4.637064 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 100pmol | 1 | 10737.953 | 13.39043 | 3.452154 | 3.452154 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 100pmol | 2 | 10655.384 | 13.37929 | 3.826245 | 3.826245 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 100pmol | 3 | 10663.714 | 13.38042 | 3.584108 | 3.584108 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 100pmol | 4 | 10843.115 | 13.40449 | 3.588195 | 3.588195 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 200pmol | 1 | 19524.863 | 14.25302 | 4.926798 | 4.926798 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 200pmol | 2 | 20072.297 | 14.29292 | 4.653112 | 4.653112 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 200pmol | 3 | 20787.127 | 14.34340 | 5.025134 | 5.025134 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 200pmol | 4 | 19924.240 | 14.28224 | 5.224020 | 5.224020 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 50pmol | 1 | 6758.298 | 12.72244 | 3.547765 | 3.547765 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 50pmol | 2 | 6721.135 | 12.71449 | 3.779592 | 3.779592 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 50pmol | 3 | 6172.877 | 12.59173 | 3.729220 | 3.729220 |
| CYC_BOVIN | CYCS | CON__P62894 | CON__P62894 | Cytochrome c | CYC_BOVIN | 50pmol | 4 | 6028.398 | 12.55756 | 3.345342 | 3.345342 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 100pmol | 1 | 13798.590 | 13.75223 | 3.813956 | 3.813956 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 100pmol | 2 | 13880.411 | 13.76076 | 4.207712 | 4.207712 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 100pmol | 3 | 13723.719 | 13.74438 | 3.948069 | 3.948069 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 100pmol | 4 | 13944.603 | 13.76742 | 3.951123 | 3.951123 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 200pmol | 1 | 24344.188 | 14.57129 | 5.245063 | 5.245063 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 200pmol | 2 | 24742.227 | 14.59469 | 4.954881 | 4.954881 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 200pmol | 3 | 24803.633 | 14.59826 | 5.279995 | 5.279995 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 200pmol | 4 | 26381.047 | 14.68721 | 5.628997 | 5.628997 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 50pmol | 1 | 7169.955 | 12.80775 | 3.633069 | 3.633069 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 50pmol | 2 | 7797.536 | 12.92880 | 3.993905 | 3.993905 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 50pmol | 3 | 7432.793 | 12.85969 | 3.997182 | 3.997182 |
| LYSC_CHICK | LYZ | P00698 | P00698 | Lysozyme C | LYSC_CHICK | 50pmol | 4 | 7543.633 | 12.88104 | 3.668827 | 3.668827 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 100pmol | 1 | 15097.670 | 13.88204 | 3.943761 | 3.943761 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 100pmol | 2 | 15840.281 | 13.95131 | 4.398260 | 4.398260 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 100pmol | 3 | 15022.215 | 13.87481 | 4.078495 | 4.078495 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 100pmol | 4 | 15160.493 | 13.88803 | 4.071733 | 4.071733 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 200pmol | 1 | 21577.973 | 14.39727 | 5.071045 | 5.071045 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 200pmol | 2 | 22968.959 | 14.48740 | 4.847591 | 4.847591 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 200pmol | 3 | 20720.127 | 14.33875 | 5.020476 | 5.020476 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 200pmol | 4 | 22153.398 | 14.43524 | 5.377023 | 5.377023 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 50pmol | 1 | 12183.812 | 13.57268 | 4.397999 | 4.397999 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 50pmol | 2 | 12521.783 | 13.61215 | 4.677255 | 4.677255 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 50pmol | 3 | 11926.220 | 13.54185 | 4.679342 | 4.679342 |
| TRFE_BOVIN | TF | CON__Q0IIK2 | CON__Q0IIK2 | Serotransferrin (UP merge to Q29443) | TRFE_BOVIN | 50pmol | 4 | 12021.495 | 13.55333 | 4.341111 | 4.341111 |