get_seqs_from_feature_df: Get sequences based on data generated with webscrape_ncbi

In Close-your-eyes/igsc: Immunoglobolin sequences from scRNAseq

Get sequences based on data generated with webscrape_ncbi

Description

Get sequences based on data generated with webscrape_ncbi

Usage

get_seqs_from_feature_df(
  feature_df,
  origin,
  concat = T,
  make_revcomp = F,
  min_to_max = F,
  return = c("sequences", "df_wide", "df_long"),
  matches_to_origin_and_feature = list(c(F, T), c(F, F)),
  order_features = F,
  compare_seq_df_long_args = list()
)

Arguments

feature_df	data frame of features as returned by webscrape_ncbi
origin	reference sequence for features
concat	concatenate sequences which have gaps in origin
make_revcomp	return the reverse complement of sequences when complement column is TRUE, for alignment to origin do not have revcomp return, for writing features into a ref genome do have the it return
min_to_max	return whole sequences from start to end including gaps (TRUE), or remove gaps (FALSE)
return	which formats to return; restriction to what is needed saves memory and increases speed
matches_to_origin_and_feature	mark matches and mismatches in origin and/or feature sequences
order_features	order features by min position
compare_seq_df_long_args

Close-your-eyes/igsc documentation built on Jan. 28, 2024, 10:28 p.m.