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EZbakRArrowData object helper function for users

EZbakRArrowData.Rd

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

Usage

EZbakRArrowData(cBds, metadf)

Arguments

cBds

ArrowDataset with the following fields:

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

  • mutational counts: Integers corresponding to the number of a particular mutation seen in a sequencing read. The following column names are allowed:

    • TC: Number of Thymine-to-Cytosine mutations

    • TA: Number of Thymine-to-Adenine mutations

    • TG: Number of Thymine-to-Guanine mutations

    • CT: Number of Cytosine-to-Thymine mutations

    • CA: Number of Cytosine-to-Adenine mutations

    • CG: Number of Cytosine-to-Guanine mutations

    • CU: Number of Cytosine-to-Uridine mutations

    • AT: Number of Adenine-to-Thymine mutations

    • AC: Number of Adenine-to-Cytosine mutations

    • AG: Number of Adenine-to-Guanine mutations

    • AU: Number of Adenine-to-Uridine mutations

    • GT: Number of Guanine-to-Thymine mutations

    • GC: Number of Guanine-to-Cytosine mutations

    • GA: Number of Guanine-to-Adenine mutations

    • GU: Number of Guanine-to-Uridine mutations

    • TN: Number of Thymine-to-Adenine/Cytosine/Guanine mutations

    • CN: Number of Cytosine-to-Adenine/Thymine/Guanine/Uridine mutations

    • AN: Number of Adenine-to-Thymine/Cytosine/Guanine/Uridine mutations

    • GN: Number of Guanine-to-Adenine/Cytosine/Thymine/Uridine mutations

    • UN: Number of Uridine-to-Adenine/Cytosine/Guanine mutations

    • NT: Number of Adenine/Cytosine/Guanine-to-Thymine mutations

    • NC: Number of Adenine/Thymine/Guanine/Uridine-to-Cytosine mutations

    • NtoA: Number of Thymine/Cytosine/Guanine/Uridine-to-Adenine mutations. (Naming convention changed because NA taken)

    • NU: Number of Cytosine/Guanine/Adenine-to-Uridine mutations.

    • NN: Number of any kind of mutation

  • base nucleotide count: Integers corresponding to the number of instances of a particular type of nucleotide whose mutations are tracked in a corresponding mutation count column. The following column names are allowed:

    • nT: Number of Thymines

    • nG: Number of Guanines

    • nA: Number of Adenines

    • nC: Number of Cytosines

    • nU: Number of Uridines

    • nN: number of any kind of nucleotide

  • features: Any columns that cannot be interpreted as a mutation count or base nucleotide count (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 cBds. This includes:

  • sample: The sample ID, which should correspond to a sample ID in the provided cBds.

  • 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 count column in the cBds 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

Value

An EZbakRArrowData object. This is simply a list of the provide cBds and metadf with class EZbakRArrowData