timeAlign-methods: Curve registration of time series curves

In Rnits: R Normalization and Inference of Time Series data

Description

Align multiple time series to the average seris

Usage

timeAlign(object, iterMax = 5, seed = 123, null.frac = 0.75,
  anchor = NULL, rerun = FALSE, plot = FALSE)

## S4 method for signature 'Rnits'
timeAlign(object, iterMax = 5, seed = 123,
  null.frac = 0.75, anchor = NULL, rerun = FALSE, plot = FALSE)

Arguments

object	rnits object
iterMax	Maximum iterations to be performed
seed	Random seed
null.frac	Fraction of genes that are considered as null
anchor	Sample to be considerded as base for aligning time series. If not provided, the average is used
rerun	If TRUE, re-align previously aligned data
plot	If TRUE, plot results

Examples

# load pre-compiled expressionSet object for Ronen and Botstein yeast  chemostat data
data(yeastchemostat)
rnitsobj = build.Rnits(yeastchemostat, logscale = TRUE, normmethod = 'Between')

# Do curve-registration on data
rnitsobj <- timeAlign(rnitsobj)

Example output

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’:

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: limma

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

    plotMA

Between Array normalization
Data set with 2 time series
Dataset with  10752  features and  2  samples in  1 replicates
Sample: 2g/l 
======Iteration Number  1 ======
Computed Adjustment for round is  26  % of cycle period
1187 1387 
Sample: 2g/l 
======Iteration Number  2 ======
Computed Adjustment for round is  23  % of cycle period
1269 1387 
Sample: 2g/l 
======Iteration Number  3 ======
Computed Adjustment for round is  21  % of cycle period
1292 1387 
Sample: 2g/l 
======Iteration Number  4 ======
Computed Adjustment for round is  21  % of cycle period
1325 1387 
###### Converged in  4 iterations ##########
Total adjustment for sample is 91 % of cycle period
 

Rnits documentation built on Nov. 8, 2020, 6:26 p.m.