filter_samples: Filter Filtered Samples by Mapping File
In erictleung/dada2HPCPipe: DADA2 HPC Workflow Wrapper

Description Usage Arguments Details Value Examples

Based on a filter criteria defined by the elements in the mapping file, this function will filter the mapping file and the associated list of sample paths.

1	filter_samples(map_file, filter, id_col_name, samples)

`map_file`	a mapping phyloseq object
`filter`	a character string with query to filter
`id_col_name`	a character string containing the ID column name in the mapping file
`samples`	a character vector

This function filters out samples in the mapping file based on some filter or metric (e.g. certain barcode sequence or group phenotype). It then gets the subset of samples from the list of sample paths and makes the list consistent with the mapping file filter.

list two attributes filtFs are paths to forward filtered sequences and filtRs are paths to reverse filtered sequences

example_forward <- c("lane1-s216-index-GTTTCTGCT-s216_L001_R1_001.fastq.gz",
                     "lane1-s217-index-CACGATGGA-s217_L001_R1_001.fastq.gz")
example_reverse <- c("lane1-s216-index-GTTTCTGCT-s216_L001_R2_001.fastq.gz",
                     "lane1-s217-index-CACGATGGA-s217_L001_R2_001.fastq.gz")
sample_names <- c("lane1-s216-index-CACGATGGA-s216",
                  "lane1-s217-index-CACGATGGA-s217")
samples <- list(forward = example_forward,
                reverse = example_reverse,
                samples= sample_names)
mapping <- data.frame(X.SampleID = c("s216"),
                      BarcodeSequence = c("AGTGATGC"),
                      Description = "Wanted sample")
filter_samples(map_file = mapping,
               filter = "BarcodeSequence == 'AGTGATGC'",
               id_col_name = "X.SampleID",
               samples = samples)