report_haplotypes: Analyse AmpSeq experiments and generate HTML reports
In bahlolab/HaplotypReportR: Generate Reports using HaplotypR

Description Usage Arguments Examples

View source: R/report_haplotypes.R

report_haplotypes performs analysis of an Ampseq experiment using the HaplotypR package. A summary of the results is presented in an HTML report with downloadable data embeded.

report_haplotypes(run_name, sample_table, marker_table, barcodes_fwd,
  barcodes_rev, reads_fwd, reads_rev, marker_panel = NULL,
  novel_hap_name = "novel", out_dir = NULL, overwrite = FALSE,
  snp_min_coverage = 100, snp_min_mismatch_rate = 0.5,
  snp_min_obs = 2, hap_sample_min_coverage = 300,
  hap_min_coverage = 3, hap_min_freq_detection = 1/100,
  parallel = "auto", max_parallel = 4, min_merge_overlap = 20,
  trim_fwd = "auto", trim_rev = "auto", trim_target_qual = 35,
  trim_target_qual_percent = 75, trim_target_len_percent = 95,
  read_join_strategy = c("auto", "bind", "merge"),
  nread_split_target = 5e+05, nread_gather_target = 50000,
  max_proc_reads = 5000, enable_forking = TRUE,
  browse_report = FALSE, marker_read_target = 1000)

`run_name`	A character scalar. Name of the AmpSeq run, included in report title.
`sample_table`	A data.frame with sample information. Must contain columns SampleID, BarcodeID_F, BarcodeID_R, SampleName.
`marker_table`	A data.frame with marker information. Must contain columns MarkerID, Forward, Reverse, ReferenceSequence.
`barcodes_fwd`	Path to fasta file containing forward barcodes. Sequence names must match `sample_table$BarcodeID_F`.
`barcodes_rev`	Path to fasta file containing reverse barcodes. Sequence names must match `sample_table$BarcodeID_R`.
`reads_fwd`	Path to fastq(.gz) file containg foward reads.
`reads_rev`	path to fastq(.gz) file containg reverse reads.
`marker_panel`	A data.frame with a panel of marker sequences (optional). Must contain columns MarkerID, Haplotype, Sequence.
`out_dir`	Path to the directory to output results.
`overwrite`	A logical scalar. Indicates whether output directory should be overwritten if it already exists.
`snp_min_coverage`	An integer scalar. Minimum read coverage required to identify a SNP in a sample.
`snp_min_mismatch_rate`	A numeric scalar. Minimum fraction of reads supporting the alternate allele required to identify as SNP in a sample. Must be between 0 and 1.
`snp_min_obs`	An integer scalar. Minimum number of times a SNP must be observed to be included in Haplotypes.
`hap_sample_min_coverage`	An integer scalar. Minimum sample marker coverage for calling Haplotypes. Passed to `HaplotypR::createFinalHaplotypTable` as `minSampleCoverage`.
`hap_min_coverage`	An integer scalar. Minimum haplotype coverage for calling Haplotypes. Passed to `HaplotypR::createFinalHaplotypTable` as `minHaplotypCoverage`.
`hap_min_freq_detection`	A numeric scalar. Minimum haplotype frequency in a sample to be reported. Must be between 0 and 1. Passed to `HaplotypR::createFinalHaplotypTable` as `detectability`.
`parallel`	An integer scalar or 'auto'. Number of processes to run in parallel using the `future` and `furrr` packages. When set to 'auto' the number of cores available will be detected.
`max_parallel`	An integer scalar. Maximum numer of processes to run in parallel.
`min_merge_overlap`	An integer scalar. Minimum number of overlapping base pairs to attempt paired read merging with `HaplotypR::mergeAmpliconReads`.
`trim_fwd`	An integer scalar or 'auto'. Number of base pairs to trim forward reads to when using `HaplotypR::bindAmpliconReads`. When set to 'auto' this will be chosen based on read quality profiles.
`trim_rev`	An integer scalar or 'auto'. See `trim_fwd`.
`trim_target_qual`	An integer scalar. Parameters controlling automatic read trimming.
`trim_target_qual_percent`	An integer scalar. Parameters controlling automatic read trimming.
`trim_target_len_percent`	An integer scalar. Parameters controlling automatic read trimming.
`read_join_strategy`	A character scalar. When set to 'auto' reads will be 'merged' if the is sufficient overlap, otherwise they will be 'bound'. When set to 'bind' reads are joined with `HaplotypR::bindAmpliconReads`. When set to 'merge' reads are joined with `HaplotypR::mergeAmpliconReads`.
`nread_split_target`	An integer scalar. Parameters controlling splitting input reads for parallelism.
`nread_gather_target`	An integer scalar. Parameters controlling splitting input reads for parallelism.
`max_proc_reads`	An integer scalar. Maximum number of reads per sample to use for genotyping. Lower values will improve runtime, higher values will improve sensitivity.
`enable_forking`	A logical scalar. Enables parallelism by forking (faster but less stable).
`browse_report`	A logical scalar. Display report in browser after run is complete.
`marker_read_target`	An integer scalar. Target number of reads per sample marker, only affects plot in report.

## Not run: 
example_data <- get_haplotypr_example_data()

report_haplotypes(run_name = 'Example',
                  sample_table = example_data$sample_table,
                  marker_table = example_data$marker_table,
                  barcodes_fwd = example_data$barcodes_fwd,
                  barcodes_rev = example_data$barcodes_rev,
                  reads_fwd = example_data$reads_fwd,
                  reads_rev = example_data$reads_rev,
                  read_join_strategy = 'bind')

## End(Not run)