quant.pd.msstats
Example of output from proteinSummarizaiton function
Bundled with MSstatsTMT · exported, loads via data()
Class
list
Elements
2
Missing
0
Format
rda · gzip
version 3 · 199 KB
File
data/quant.pd.msstats.rda
Fingerprint
f5212181
Format documented
Yes
Source
Source not stated
About this object
R's general-purpose container. Elements can be any type and any size. R object catalogue
Structure
Distinct
2
Nesting depth
2
Element length
8 – 13
Total length
21
Nested rows
21,560
Nested columns
13
Nested schema
varies between elements
Elements
Element
Type
Distinct
Missing
Summary
FeatureLevelDatalist130nested·20,360 rows nested
Element length
20,360 – 20,360
Total length
264,680
Nested rows
20,360
What is inside it
Element
Type
Distinct
Missing
Summary
ProteinNamefactor100P044064,580P065764,090Q152333,280Q9NSD91,930P122771,770Q161811,550+4 more
P044064,580P065764,090Q152333,280Q9NSD91,930P122771,770Q161811,550+4 more
Levels
10
Used
10
Rows per level
P044064,580P065764,090Q152333,280Q9NSD91,930P122771,770Q161811,550P239191,010P31947990Q9UGP8730Q9Y450430
PSMfactor3050[K].aLIEMEk.[Q]_2150[K].aNWEAQQr.[I]_2150[K].dSEAELQr.[R]_2150[K].fEDYLNAESr.[V]_2150[K].lAVEALSSLDGDLAGr.[Y]_3150[K].lEMEMEAAr.[H]_2150+299 more
[K].aLIEMEk.[Q]_2150[K].aNWEAQQr.[I]_2150[K].dSEAELQr.[R]_2150[K].fEDYLNAESr.[V]_2150[K].lAVEALSSLDGDLAGr.[Y]_3150[K].lEMEMEAAr.[H]_2150+299 more
Levels
305
Used
305
Rows per level, the 50 commonest of 305
[K].aLIEMEk.[Q]_2150[K].aNWEAQQr.[I]_2150[K].dSEAELQr.[R]_2150[K].fEDYLNAESr.[V]_2150[K].lAVEALSSLDGDLAGr.[Y]_3150[K].lEMEMEAAr.[H]_2150[K].qASEGPLk.[G]_2150[K].rVIISAPSADAPMFVmGVNHEk.[Y]_4150[K].sLQDIIAILGmDELSEEDk.[L]_3150[K].tFLVWVNEEDHLr.[V]_3150[K].tVDGPSGk.[L]_2150[K].vGVNGFGr.[I]_2150[K].vLDSGAPIk.[I]_2150[K].wGDAGAEYVVESTGVFTTmEk.[A]_3150[K].wGDAGAEYVVESTGVFTTMEk.[A]_3150[R].hEHQVMLmr.[Q]_4150[R].lVLEVAQHLGESTVr.[T]_3150[R].tIAMDGTEGLVr.[G]_2150[R].vVDLmAHMASk.[E]_3150[K].aGAHLQGGAk.[R]_3140[K].gEELScEEr.[N]_2140[K].iISNAScTTNcLAPLAk.[V]_3140[K].rVIISAPSADAPMFVMGVNHEk.[Y]_4140[K].tVLIMELINNVAk.[A]_3140[R].dQNAEQIr.[L]_2140[R].eVLGDAVPDEILIEAVLk.[N]_3140[R].fLSQPFQVAEVFTGHMGk.[L]_3140[R].gAFGHEr.[Y]_3140[R].gALQNIIPASTGAAk.[A]_3140[R].hLcAVYYNk.[N]_3140[R].iLEQQNSSr.[T]_2140[R].iMDPNIVGSEHYDVAr.[G]_3140[R].lFVGNLPPDITEEEMr.[K]_2140[R].vIISAPSADAPMFVMGVNHEk.[Y]_3140[R].vLLLSHLAr.[M]_3140[R].vVDLMAHmASk.[E]_3140[R].vVDLMAHMASk.[E]_3140[R].yENGAFQEr.[A]_2140[K].lVEALcAAGHr.[A]_3140[R].hEHQVmLMr.[Q]_4140[K].dTTLNWk.[M]_2130[K].lHQNIcr.[K]_3130[K].lISWYDNEFGYSNr.[V]_3130[K].lVINGNPITIFQEr.[D]_3130[K].qQQDQVDr.[N]_2130[K].rDLLFQALGr.[T]_3130[K].rGTGGVDTAAVGGVFDVSNADr.[L]_3130[K].sLQDIIAILGMDELSEEDk.[L]_3130[K].vELDNMPLr.[G]_2130[K].vETELQGVcDTVLGLLDSHLIk.[E]_3130
censored
logical
2
0
180 true·20,180 false
predictednumeric18020,1808.2168 – 15.7924mean 10.46
Min.
8.2168
1st Qu.
9.1132
Median
9.4268
Mean
10.4568
3rd Qu.
11.397
Max.
15.7924
Std. dev
1.9743
Skewness
1.066
Kurtosis
-0.1264
Outliers
60 low · 6 high
Longest gap
1,041
Leading
159
Trailing
45
log2Intensitynumeric20,23107.9447 – 24.0437mean 15.16
Min.
7.9447
1st Qu.
13.5206
Median
15.2156
Mean
15.1609
3rd Qu.
16.7979
Max.
24.0437
Std. dev
2.4215
Skewness
0.0275
Kurtosis
-0.0328
Outliers
13030 low · 100 high
Run
character
15
0
43 characters
Channel
character
10
0
3 – 4 characters
BioReplicate
character
5
0
1 – 5 characters
Condition
factor
5
0
0.1254,0720.54,0720.6674,07214,072Norm4,072
Mixture
character
5
0
8 characters
TechRepMixture
character
3
0
1 characters
PeptideSequence
character
228
0
15 – 49 characters
Charge
character
4
0
1 characters
ProteinLevelDatalist80nested·1,200 rows nested
Element length
1,200 – 1,200
Total length
9,600
Nested rows
1,200
What is inside it
Element
Type
Distinct
Missing
Summary
Mixture
factor
5
0
Mixture1240Mixture2240Mixture3240Mixture4240Mixture5240
TechRepMixture
factor
3
0
140024003400
Runfactor150161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw80+9 more
161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw80+9 more
Levels
15
Used
15
Rows per level
161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02raw80161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03raw80
Channelfactor80127C150127N150128C150128N150129C150129N150+4 more
127C150127N150128C150128N150129C150129N150+4 more
Levels
10
Used
8
Unused
2
Rows per level, the 8 commonest of 10
127C150127N150128C150128N150129C150129N150130C150130N150
Proteinfactor100P04406120P06576120P12277120P23919120P31947120Q15233120+4 more
P04406120P06576120P12277120P23919120P31947120Q15233120+4 more
Levels
10
Used
10
Rows per level
P04406120P06576120P12277120P23919120P31947120Q15233120Q16181120Q9NSD9120Q9UGP8120Q9Y450120
Abundancenumeric1,200012.4537 – 16.9684mean 14.86
Min.
12.4537
1st Qu.
14.1454
Median
14.9816
Mean
14.8647
3rd Qu.
15.449
Max.
16.9684
Std. dev
0.9529
Skewness
-0.1616
Kurtosis
-0.4094
BioReplicate
character
4
0
1 – 5 characters
Condition
factor
4
0
0.1253000.53000.6673001300
The nested tables do not share one set of columns, so there is no single schema to show.
Version history
| Version | Released | Size | Change | Stored as | Confidence |
|---|---|---|---|---|---|
| 3.23 | 2026-04-28 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.22 | 2025-10-29 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.21 | 2025-04-15 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.20 | 2025-03-05 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.19 | 2024-05-20 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.18 | 2023-10-24 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.17 | 2023-04-25 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.16 | 2023-02-26 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.15 | 2022-09-12 | 2 elements | Unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.14 | 2022-02-18 | 2 elements | Data changed Class, Type, Missing and Distinct unchanged | rda · gzip version 3 · 199 KB | exact |
| 3.13 | 2021-06-14 | 2 elements | Data changed Class data.frame → list | rda · gzip version 3 · 201 KB | exact |
| 3.12 | 2020-12-20 | 1,200 × 8 | Unchanged | rda · gzip version 3 · 13 KB | exact |
| 3.11 | 2020-10-13 | 1,200 × 8 | Unchanged | rda · gzip version 3 · 13 KB | exact |
| 3.10 | 2020-04-14 | 1,200 × 8 | Unchanged | rda · gzip version 3 · 10.0 KB | exact |
| 3.9 | 2019-05-04 | 1,200 × 8 | Data changed Dimensions 1,500 × 7 → 1,200 × 8 | rda · gzip version 3 · 10.0 KB | exact |
| 3.8 | 2019-02-25 | 1,500 × 7 | – | rda · gzip version 2 · 13 KB | exact |
Dimensions is the row and column count. Class is the chain of classes R records on the object, most specific first. The facts above give the short name for the same chain. Type is what the values in it are. Missing is how many values were recorded as absent. Distinct is how many different values were counted in the object.