Man pages for carlopacioni/amplicR
An R package to process amplicon data
| AIC | AIC |
| AIC.comp | Compute and compare AIC for different fasimcoal models |
| amplicR | amplicR |
| collate.seqs | Collate sequences |
| dart2nexus | Convert SNPs data from a genlight object (from Dart... |
| data.proc | Data processing |
| data.proc.paired | Data processing - paired ends |
| deconv | Separate reads by genes and deconvolute them based on... |
| detect | Detect a reference sequence |
| fsc.bootstraps | Compute bootstrap confidence intervals for estimated... |
| fsc.estimate | Run fastsimcoal to estimate parameters' values |
| fsc.multiple.estimate | Run fsc over multiple models |
| getnFiltered | Return the number of filtered sequences from a derep obj |
| getnUniques | Return the number of unique sequences in a derep obj |
| getRow | Extracts rows from a matrix into a vector |
| getSeqFromDerep | Extract sequences from a derep object |
| gl2sfs | Convert a genlight object into a sfs input file |
| make.alleles | Build (possible) allele sequences based on genotypes |
| make.phyloseq | Create a phyloseq object |
| ndada | Return the number of unique sequences in a dada obj |
| putna | Replace null values with NA |
| putzero | Replace null values with zero or x with x - 1 |
| raw2data.proc | From raw data to data.proc() |
| replaceSNP | Replace SNPs with IUPAC ambiguities |
| rmEndAdapter | Remove end adapter |
| sel.match | Select appropriate hits when searching a patter |
| setup | Set up environment to use 'amplicR' |
| subsetDerep | Subset a derep-class based on abundance of the reads |
| table2fasta | Write unique sequences to a fasta file for each sample where... |
| where2trim | Select position where a pattern has been found |
| write.nexus | Write a nexus file from a DNAStringSet object |
