chimera_removal_vs {MiscMetabar}R Documentation

Search for a list of sequence in an object to remove chimera taxa using vsearch

Description

[Experimental]

Usage

chimera_removal_vs(object, type = "Discard_only_chim", clean_pq = FALSE, ...)

Arguments

object

(required) A phyloseq-class object or one of dada, derep, data.frame or list coercible to sequences table using the function dada2::makeSequenceTable()

type

(default "Discard_only_chim"). The type define the type of filtering.

  • "Discard_only_chim" will only discard taxa classify as chimera by vsearch

  • "Select_only_non_chim" will only select taxa classify as non-chimera by vsearch(after filtering taxa based on their sequence length by the parameter min_seq_length from the chimera_detection_vs() function)

  • "Select_only_chim" will only select taxa classify as chimera by vsearch (after filtering taxa based on their sequence length by the parameter min_seq_length from the chimera_detection_vs() function)

clean_pq

(logical; default FALSE) If TRUE, return the phyloseq object after cleaning using the default parameter of clean_pq() function.

...

Others arguments passed on to chimera_detection_vs() function

Details

This function is mainly a wrapper of the work of others. Please make vsearch.

Value

Author(s)

Adrien Taudière

See Also

chimera_detection_vs()

Examples



data_fungi_nochim <- chimera_removal_vs(data_fungi)
data_fungi_nochim_16 <- chimera_removal_vs(data_fungi,
  abskew = 16,
  min_seq_length = 10
)
data_fungi_nochim2 <-
  chimera_removal_vs(data_fungi, type = "Select_only_non_chim")
data_fungi_chimera <-
  chimera_removal_vs(data_fungi, type = "Select_only_chim")



[Package MiscMetabar version 0.9.1 Index]