Get indexes of sequences parsed by sample — xdev_get_sequence_indexes_by

As a developer you may want to process data by sample. To save space you can request the indexes parsed by sample, and then get a single copy of the sequences and sequence names.

Usage

xdev_get_sequence_indexes_by_sample(data, samples = as.character(c()))

Arguments

data: a strollur object
samples: a vector of strings containing the names of the samples you would like sequence names for. By default all samples are included.

Value

2D vector of strings indexes for use with xdev_get_sequences and xdev_get_names. requested parsed by sample. (Indexes start at 1)

Examples


data <- strollur::miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 171 samples distances.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added a metadata report.
#> Added 2 resource references.
#> Added a contigs_report report.

sequences <- strollur::xdev_get_sequences(data)
names <- strollur::xdev_names(data)

# To get the indexes of the names and sequences by sample
indexes <- strollur::xdev_get_sequence_indexes_by_sample(data)

# First sequence in first sample
names[indexes[[1]][1]]
#> [1] "M00967_43_000000000-A3JHG_1_2103_25452_6018"
sequences[indexes[[1]][1]]
#> [1] "TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GTGGC-G-CA-GGC-G-G-G-AT-G-C-C--A-G-T-C-A-G-C-G-G--TC-A-AA-TT-T-C-GG-GG--CT-C-AA-C-C-C-C-G-A-C--CT-G-C-CGTT-GAAAC-TG-G-TGTCC-TAGA-GT-GG-GC-GA-G-A---AG-T-A-TGCGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CC-C-G-ACTGACG-CTCA-TGCA-CGAAA-GCG-TGGGT-ATC-GAACAGG"