sos: SOS pathway time series data

In SPEM: S-system parameter estimation method

Description

In this package we offer the SOS data obtained from Uri Alon's lab (http://www.weizmann.ac.il/mcb/UriAlon/). SOS response is a general DNA repair system in bacteria which allows survival after DNA damage. This SOS dataset is taken from real experiment expression data in Escherichia coli. It contains 8 genes under Experiment 3 (UV light intensities, 4:20 Jm^(-2)).

Usage

data(sos)

Format

sos.data is time series gene expression value data in ExpressionSet Class. assayData: Matrix with expression values of 8 genes in SOS pathway of Escherichia coli. These expression levels are observed at 50 time points. phenoData: Sample data.frame includes label "time", which represents the value of time points.

References

M. Ronen, R. Rosenberg, B. I. Shraiman, and U. Alon. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proceedings of the National Academy of Sciences of the United States of America, Aug. 2002. PMID: 12145321.

Examples

data(sos)

Example output

Loading required package: Rsolnp
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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SPEM documentation built on Nov. 8, 2020, 6:52 p.m.