In amplicon filtering it is sometimes valuable to compare technical
replicates in order to estimate the accuracy of a genotyping experiment. This
may be done both to optimize filtering settings and to estimate repeatability
to report in a publication. ReplMatch is designed to
automatically compare technical replicates in an amplicon filtering data set
and report the proportion of mismatches. The functions GetReplTable() and
GetReplStats() are designed to evaluate the output files.
ReplMatch(repl_table, seq_table, path_out)is a table containing the sample names of technical replicates in the data set. This table should be organized so that the individual names are in the first column (Sample_ID), and the index number of the replicate set is in the second column (Replic_set). Replicate sets are allowed to contain more than two replicates. It is assumed that replicate sets are numbered consecutively beginning at 1.
seq_table is a sequence table as output by the 'dada2' pipeline, which has samples in rows and nucleotide sequence variants in columns.
is a user defined path to the folder where the output files will be saved.
A set of R lists containing for each replicate set the observed sequence variants, the names of the sequences that were incongruent in the replicates, and the mean proportion of incongruent sequences (if 100 matches are expected between the replicates, this is equivalent of an error rate in the sequencing process). The sequences are named in the output by an index number corresponding to their column number in the sequence table, thus identical sequences will have identical sample names in all the output files. These files can be reopened in R using e.g. the list.load() function in the 'rlist' package.
GetReplTable; GetReplStats; for more
information about 'dada2' visit <https://benjjneb.github.io/dada2>
# NOT RUN {
repl_table <- replicates_table
seq_table <- sequence_table_repl
path_out <- tempdir()
ReplMatch(repl_table, seq_table, path_out)
# }
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