strollur 0.1.4

New Features:

• Expands built in read / write functions.
  • strollur::read_fastq() returns data.frame with fastq data.
  • strollur::write_fastq() writes fastq data to file.
  • strollur::read_quality() returns data.frame with sequence quality data.
  • strollur::write_quality() writes sequence quality data to file.
  • strollur::read_biom() returns a strollur_object.
  • strollur::write_biom() writes biom files containing the strollur_object.
• Expands member functions of the strollur_object.
  • strollur_object$alignment_length() returns the sequences alignment length or -1 if the sequences are unaligned.
  • strollur_object$has_bin_taxonomy() returns TRUE if your dataset includes bin classifications.
  • strollur_object$has_sequence_taxonomy() returns TRUE if your dataset includes sequence classifications.
  • strollur_object$rename() rename the strollur object.

Enhancements:

• Adds fastq, quality, sequence_tree, sample_tree, sample_distance types to:
  • strollur::report()
  • strollur_object$report()
• Adds fastq type to:
  • strollur::add()
  • strollur_object$add()
• Adds quality and sample_distance type to:
  • strollur::assign()
  • strollur_object$assign()

Functions for Package developers

• Adds strollur::xdev_add_sequence_fastq_scores() function.
• Adds strollur::xdev_alignment_length() function
• Adds strollur::xdev_assign_bin_taxonomy_tidy() function.
• Adds strollur::xdev_assign_sample_distances() function.
• Adds strollur::xdev_assign_sequence_quality_scores function.
• Adds strollur::xdev_has_bin_taxonomy() function.
• Adds strollur::xdev_get_sample_distances() function.
• Adds strollur::xdev_get_sequence_indexes_by_sample() function.

Bug Fixes: - strollur::summary() will now display results that accurately represent the data.

Deprecated:

• Simplifies member functions of the strollur_object.
  • Removes strollur_object$add_sequence_tree() : Functionality now included instrollur_object$add().
  • Removes strollur_object$add_sample_tree() : Functionality now included instrollur_object$add().
  • Removes strollur_object$get_sequence_tree() : Functionality now included instrollur_object$report().
  • Removes strollur_object$get_sample_tree() : Functionality now included instrollur_object$report().

strollur 0.1.3

• Adds strollur::read_mothur_oligos() function for the import of oligo data from mothur.
• Makes report format more flexible. You can now add reports that are not tied to sequence data. These can be general metadata, oligo information, paired fastq file tables and much more.

strollur 0.1.2

• Initial CRAN release.