imp4p: pi_mcar_karpievitch – R documentation

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pi_mcar_karpievitch

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.

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)

imp4p

Imputation for Proteomics

v1.1

GPL-3

Authors

Quentin Giai Gianetto

Initial release