Wrapper to fetch sequences from the archR result object as character
seqs_str(res, iter = NULL, cl = NULL, ord = FALSE)
| res | archR result object |
|---|---|
| iter | Specify the iteration of archR result. If set to NULL (the default), the original set of sequences (`archRresult$rawSeqs`) is returned. |
| cl | Specify the cluster number. Sequences belonging to this cluster in iteration `iter` of archR result are returned as character. When `iter` is NULL, this is treated as denoting the cluster number in archR's final clustering solution (`archRresult$clustSol$clusters`). |
| ord | Specify TRUE if sequences are ordered by clusters. The original ordering of the sequences can be fetched by setting `iter` to NULL and `ord` to FALSE. |
The selected DNA sequences from the DNAStringSet object as a character vector.
Setting iter to NULL will fetch sequences as per the final clustering solution of archR (`clustSol$clusters`). When `iter` is not NULL, use `cl` to further choose a particular cluster. When `cl` is NULL, the set of sequences returned can be ordered by clusters with `ord = TRUE`. Using `ord = FALSE` fetches the sequences by their original order.
res <- system.file("extdata", "example_archRresult.rds", package = "archR", mustWork = TRUE) # Fetch sequences from 2nd cluster of archR's final solution ans <- archR::seqs_str(readRDS(res), iter=NULL, cl=2) # Fetch all sequences ordered by the final clustering ans <- archR::seqs_str(readRDS(res), iter=NULL, cl=NULL, ord=TRUE) # Fetch sequences belonging to first cluster in archR's first iteration ans <- archR::seqs_str(readRDS(res), iter=1, cl=1)