Data: Constructor function for S3 class representing an NGS Data...

In PoonLab/highlineR: A Novel Visualization Tool to Assess Diversity in NGS Data

Description

Data returns constructed Data object.

Usage

Data(path, datatype = utils::tail(strsplit(path, "\\.")[[1]], n = 1),
  seqtype = "nucleotide")

Arguments

path	A character string representing the absolute path to sequence file.
datatype	A character string representing the file type. Default value is file extension (last of all period (".") separated extensions).
seqtype	A character string representing the sequence type. Options: "nucleotide" (default) or "amino acid".

Value

Returns a constructed S3 object which is a child object of a parent session object, inherits from the following classes:

• datatype: The file type of NGS file represeted by the object.

• seqtype: The sequence type of the sequences in the NGS file represeted by the object.

• Data.

• environment.

and contains the following elements:

• path: The absolute path to the NGS file represented by the object.

• raw_seq: A list that will contain the parsed sequences of the NGS file.

• compressed: An S3 object that inherits from the base environment class and will contain the compressed sequences of the NGS file.

• sample: An S3 object that inherits from the base environment class and will contain randomly sampled sequences from the the compressed structure.

• master: A character string representing the master sequence to use for plotting.

• seq_diff: A character matrix of sequence differences in variant sequences compared to the master sequence.

PoonLab/highlineR documentation built on Aug. 2, 2019, 4:32 p.m.