R: Estimating the proportion of MCAR values in biological...

pi.mcar.karpievitch {imp4p} | R Documentation

## Estimating the proportion of MCAR values in biological conditions using the method of Karpievitch (2009).

### Description

This function allows estimating the proportion of MCAR values in biological conditions using the method of Karpievitch (2009).

### Usage

    pi.mcar.karpievitch(tab,conditions)

### Arguments

`tab` | A data matrix containing numeric and missing values. Each column of this matrix is assumed to correspond to an experimental sample, and each row to an identified peptide.
`conditions` | A vector of factors indicating the biological condition to which each column (experimental sample) belongs.

### Value

A list composed of:

`pi.mcar` | The proportion of MCAR values in each biological condition.
`prop.na` | The proportion of missing values for each peptide in each condition.
`moy` | The average of observed values for each peptide in each condition.

### Author(s)

Quentin Giai Gianetto <quentin2g@yahoo.fr>

### References

Karpievitch, Y., Stanley, J., Taverner, T., Huang, J., Adkins, J. N., Ansong, C., ... & Smith, R. D. (2009). A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics, 25(16), 2028-2034.

### See Also

`estim.mix`

### Examples

    #Simulating data
    res.sim=sim.data(nb.pept=2000,nb.miss=600);

    #Proportion of MCAR values in each condition
    pi.mcar.karpievitch(tab=res.sim$dat.obs,conditions=res.sim$conditions)

[Package imp4p version 1.1 Index]