seqs_str: Get sequences from the archR result object

In snikumbh/archR: Identify Different Architectures of Sequence Elements

Description

Wrapper to fetch sequences from the archR result object as character

Usage

seqs_str(res, iter = NULL, cl = NULL, ord = FALSE)

Arguments

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.

Details

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.

Value

The selected DNA sequences from the DNAStringSet object as a character vector.

Examples

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)

snikumbh/archR documentation built on July 5, 2021, 8:46 a.m.