Read a mothur formatted count file
Examples
# mothur count file
# Representative_Sequence total sample2 sample3 sample4
# seq1 1150 250 400 500
# seq2 115 25 40 50
# seq3 50 25 25 0
# seq4 4 0 0 4
# returns
# id sample abundance
# <char> <char> <int>
# 1: seq1 sample2 250
# 2: seq1 sample3 400
# 3: seq1 sample4 500
# 4: seq2 sample2 25
# 5: seq2 sample3 40
# 6: seq2 sample4 50
# 7: seq3 sample2 25
# 8: seq3 sample3 25
# 9: seq4 sample4 4
# read a count file with samples
sample_table <- read_mothur_count(strollur_example("final.count_table.gz"))
# You can add your sequence abundance data to your `strollur` object as
# follows:
# create a new empty `strollur` object
data <- new_dataset()
# assign sequence abundances parsed by sample
assign(data, table = sample_table, type = "sequence_abundance")
#> Assigned 2425 sequence abundances.
#> [1] 2425
# print summary of data
data
#>
#> Number of unique seqs: 2425
#> Total number of seqs: 113963
#>
#> Total number of samples: 19
#>