get_time_series_df_bio: Extracts a time series data frame from a Bioconductor Biobase...

In TMixClust: Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Description

get_time_series_df_bio creates a data frame with time series data from a Bioconductor Biobase ExpressionSet object.

Usage

get_time_series_df_bio(bio_obj)

Arguments

bio_obj

Bioconductor Biobase ExpressionSet object. The assayData has to contain a matrix where each row is a gene time series and each column contains the time series values at each time point. The number of columns is equal to the number of time points, while the number of rows is equal to the number of genes.

Value

A data frame containing the time series

Author(s)

Monica Golumbeanu, [e-mail]

References

Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. (2017) Dynamics of Proteo-Transcriptomic Response to HIV-1 Infection.

Examples

# Load the SOS pathway data from Bioconductor package SPEM
library(SPEM)
data(sos)
sos_data = get_time_series_df_bio(sos)

# Print the first lines of the retrieved time series data frame
print(head(sos_data))

TMixClust documentation built on Nov. 8, 2020, 8:13 p.m.