EZbakRFractions helper function for users

EZbakRFractions creates an object of class EZbakRFractions and checks the validity of the provided input.

Usage

EZbakRFractions(fractions, metadf, name = NULL, character_limit = 20)

Arguments

fractions

Data frame with the following columns:

• sample: Name given to particular sample from which data was collected.

• estimates of population fractions: These columns refer to the estimate for the fraction of reads coming from a particular mutational population. For example, in a standard NR-seq experiment, you should have one column named fraction_highTC. This refers to the fraction of RNA inferred to have a high T-to-C mutation rate (e.g., the newly synthesized RNA in a pulse-labeling NR-seq experiment). If you estimated the fractions of more than 2 mutation types (e.g., T-to-C and G-to-A), then you need to explicitly list all fractions of interest estimated. For example, in a TILAC experiment, this would be fraction_highTC_lowGA, fraction_lowTC_highGA, and fraction_lowTC_lowGA.

• n: Number of reads assigned to a given feature in a given sample.

• features: Any columns that cannot be interpreted as an estimate of population fractions (and that aren't named sample or n) will be interpreted as an ID for a genomic "feature" from which a read originated. Common examples of features and typical column names for said features include:

  • Genes; common column names: gene, gene_id, gene_name, GF

  • Genes-exonic; common column names: gene_exon, gene_id_exon, gene_name_exon, XF

  • Transcripts; common column names: transcripts, TF

  • Exonic bins; common column names: exonic_bins, EF, EB

  • Exons; common column names: exons, exon_ids

  In some cases, a read will often map to multiple features (e.g., exons). Many functions in bakR expect each of the feature IDs in these cases to be separated by +. For example, if a read overlaps with two exons, with IDs exon_1 and exon_2, then the corresponding entry in a column of exonic assignments would be "exon_1+exon_2". The default expectation can be overwritten though and is thus not strictly enforced.

• n: Number of reads with identical values for all other columns.

metadf

Data frame detailing various aspects of each of the samples included in the fractions data frame. This includes:

• sample: The sample ID, which should correspond to a sample ID in the provided fractions data frame.

• tl: Metabolic label time. There are several edge cases to be aware of:

  • If more than one metabolic label was used in the set of samples described by the metadf (e.g., s4U and s6G were used), then the tl column should be replaced by tl_<muttype>, where <muttype> represents the corresponding mutation type referenced in the fractions that the label whose incubation time will be listed in this column. For example, if feeding with s4U in some samples and s6G in others, then performing standard nucleotide recoding chemistry, you will include tl_TC and tl_GA columns corresponding to the s4U and s6G label times, respectively.

  • If a pulse-chase experimental design was used (!!this is strongly discouraged unless you have a legitimate reason to prefer this design to a pulse-label design!!), then you should have columns named tpulse and tchase, corresponding to the pulse and chase times respectively. The same _ convention should be used in the case of multi-label pulse-chase designs.

• sample characteristics: The remaining columns can be named whatever you like and should include distinguishing features of groups of samples. Common columns might include:

  • treatment: The experimental treatment applied to a set of samples. This could represent things like genetic knockouts or knockdowns, drug treatments, etc.

  • batch: An ID for sets of samples that were collected and/or processed together. Useful for regressing out technical batch effects

name

Optional; name to give to fractions table.

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.

Value

An EZbakRFractions object. This is simply a list of the provide fractions and metadf with class EZbakRFractions