medianSummary: summarize peptide/PSM intensity into protein level relative...
In yafeng/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 median method
Usage
1
medianSummary(dat,group_col=2,ref_col)
Arguments
dat
an data frame with peptide/psm intensities in log2 scale
group_col
the column by which peptides/psm intensity are grouped.
Usually the gene/protein id column. Default is 2
ref_col
an integer vector indicating the column(s) used as denominator
to calcualte relative petide ratio.
Value
a data frame containing protein relative abundance estimate in log2 scale
Author(s)
Yafeng Zhu
Examples
1
2
3
4
5
6
7
8
9
library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]
dat.psm.log = dat.psm
dat.psm.log[,3:12] = log2(dat.psm[,3:12])
# use the 3 ctrl samples as reference channels to calculate log2 ratio
dat.gene = medianSummary(dat.psm.log,group_col = 2,ref_col =c(3,7,10))
yafeng/DEqMS documentation built on June 3, 2020, 8:23 p.m.
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.
Description Usage Arguments Value Author(s) Examples
Description
This function is to calculate proteins'relative abundance by median method
Usage
1 | medianSummary(dat,group_col=2,ref_col)
|
Arguments
dat |
an data frame with peptide/psm intensities in log2 scale |
group_col |
the column by which peptides/psm intensity are grouped. Usually the gene/protein id column. Default is 2 |
ref_col |
an integer vector indicating the column(s) used as denominator to calcualte relative petide ratio. |
Value
a data frame containing protein relative abundance estimate in log2 scale
Author(s)
Yafeng Zhu
Examples
1 2 3 4 5 6 7 8 9 | library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]
dat.psm.log = dat.psm
dat.psm.log[,3:12] = log2(dat.psm[,3:12])
# use the 3 ctrl samples as reference channels to calculate log2 ratio
dat.gene = medianSummary(dat.psm.log,group_col = 2,ref_col =c(3,7,10))
|
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.