Generic function for estimating kinetic parameters.

Usage

EstimateKinetics(
  obj,
  strategy = c("standard", "tilac", "NSS", "shortfeed", "pulse-chase"),
  features = NULL,
  populations = NULL,
  fraction_design = NULL,
  repeatID = NULL,
  exactMatch = TRUE,
  grouping_factor = NULL,
  reference_factor = NULL,
  character_limit = 20,
  feature_lengths = NULL,
  overwrite = TRUE
)

Arguments

obj

An EZbakRFractions object, which is an EZbakRData object on which EstimateFractions() has been run.

strategy

Kinetic parameter estimation strategy. Options include:

standard: Estimate a single new read and old read mutation rate for each sample. This is done via a binomial mixture model aggregating over
NSS: Use strategy similar to that presented in Narain et al., 2021 that assumes you have data which provides a reference for how much RNA was present at the start of each labeling. In this case, grouping_factor and reference_factor must also be set.
shortfeed: Estimate kinetic parameters assuming no degradation of labeled RNA, most appropriate if the metabolic label feed time is much shorter than the average half-life of an RNA in your system.
tilac: Estimate TILAC-ratio as described in Courvan et al., 2022.
pulse-chase (NOT YET IMPLEMENTED): Estimate kdeg for a pulse-chase experiment. A kdeg will be estimated for each time point at which label was present. This includes any pulse-only samples, as well as all samples including a chase after the pulse.
custom (NOT YET IMPLEMENTED): Provide a custom function that takes fraction estimates as input and produces as output kinetic parameter estimates.

features

Character vector of the set of features you want to stratify reads by and estimate proportions of each RNA population. The default of "all" will use all feature columns in the obj's cB.

populations

Mutational populations that were analyzed to generate the fractions table to use. For example, this would be "TC" for a standard s4U-based nucleotide recoding experiment.

fraction_design

"Design matrix" specifying which RNA populations exist in your samples. By default, this will be created automatically and will assume that all combinations of the mutrate_populations you have requested to analyze are present in your data. If this is not the case for your data, then you will have to create one manually. See docs for EstimateFractions (run ?EstimateFractions()) for more details.

repeatID

If multiple fractions tables exist with the same metadata, then this is the numerical index by which they are distinguished.

exactMatch

If TRUE, then features and populations have to exactly match those for a given fractions table for that table to be used. Means that you can't specify a subset of features or populations by default, since this is TRUE by default.

grouping_factor

Which sample-detail columns in the metadf should be used to group samples by for calculating the average RPM at a particular time point? Only relevant if strategy = "NSS".

reference_factor

Which sample-detail column in the metafd should be used to determine which group of samples provide information about the starting levels of RNA for each sample? This should have values that match those in grouping_factor. #' Only relevant if strategy = "NSS".

character_limit

Maximum number of characters for naming out fractions output. EZbakR will try to name this as a "_" separated character vector of all of the features analyzed. If this name is greater than character_limit, then it will default to "fraction#", where "#" represents a simple numerical ID for the table.

feature_lengths

Table of effective lengths for each feature combination in your data. For example, if your analysis includes features named GF and XF, this should be a data frame with columns GF, XF, and length.

overwrite

If TRUE and a fractions estimate output already exists that would possess the same metadata (features analyzed, populations analyzed, and fraction_design), then it will get overwritten with the new output. Else, it will be saved as a separate output with the same name + "_#" where "#" is a numerical ID to distinguish the similar outputs.

Value

EZbakRKinetics object.