farmsSummary: summarize peptide/PSM intensity into protein level relative...
In DEqMS: a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
Description
Usage
Arguments
Value
Author(s)
Examples
Description
This function is to calculate proteins'relative abundance by factor analysis
Usage
1
farmsSummary(dat,group_col=2)
Arguments
dat
an data frame with raw peptide or psm intensities
group_col
the column by which peptides/psm intensity are grouped.
Usually it is the gene/protein id column. Default is 2
Value
a data frame containing protein relative abundance estimate in log2 scale
Author(s)
Yafeng Zhu
Examples
1
2
3
4
5
6
library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]
# farms method does not tolerate missing values
dat.gene = farmsSummary(dat.psm,group_col=2)
DEqMS documentation built on Nov. 8, 2020, 7:51 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
This function is to calculate proteins'relative abundance by factor analysis
Usage
1 | farmsSummary(dat,group_col=2)
|
Arguments
dat |
an data frame with raw peptide or psm intensities |
group_col |
the column by which peptides/psm intensity are grouped. Usually it is the gene/protein id column. Default is 2 |
Value
a data frame containing protein relative abundance estimate in log2 scale
Author(s)
Yafeng Zhu
Examples
1 2 3 4 5 6 | library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]
# farms method does not tolerate missing values
dat.gene = farmsSummary(dat.psm,group_col=2)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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