estimate_log_fold_change: Estimates log fold change

In NelleV/moanin: An R Package for Time Course RNASeq Data Analysis

Description

Estimates log fold change

Usage

## S4 method for signature 'Moanin'
estimate_log_fold_change(
  object,
  contrasts,
  method = c("timecourse", "sum", "max", "timely", "abs_sum", "abs_squared_sum", "min")
)

Arguments

object	An object of class Moanin, an object containing all related information for time course data and the splines model that will be used (if applicable). See create_moanin_model for more details.
contrasts	The contrasts to consider
method	method for calculating the log-fold change. See details.

Details

The following methods exist for calculating the log-fold change between conditions over time (default is "timecourse"):

• timelyThe log-fold change for each individual timepoint (lfc(t))

• timecourseThe average absolute per-week fold-change, multiplied by the sign of the average per-week fold-change.

• sumSum of per-week log fold change, over all timepoints

• maxMax of per-week log fold change, over all timepoints

• abs_sumSum of the absolute value of the per-week log fold change, over all timepoints

• abs_squared_sumSum of the square value of the per-week log fold change, over all timepoint

• minMin of per-week log fold change, over all timepoints

If the user set log_transform=TRUE in the creation of the Moanin object, the data will be log transformed before calculating the fold-change.

Value

A data.frame giving the estimated log-fold change for each gene (row). For all methods except for "timely", the data frame will consist of one column for each value of the argument contrasts. For "timely" there will be one column for each timepoint and contrast combination.

Examples

data(exampleData)
moanin <- create_moanin_model(data=testData,meta=testMeta)
estsTimely <- estimate_log_fold_change(moanin, 
   contrasts=c("K-C"), method="timely")
head(estsTimely)
estsTimecourse <- estimate_log_fold_change(moanin, 
   contrasts=c("K-C"),method="timecourse")
head(estsTimecourse)

NelleV/moanin documentation built on July 28, 2021, 7:34 p.m.