subdivide_data: Subdivides Sequences into _n_ Bins
In kkrismer/transite: RNA-binding protein motif analysis

subdivide_data

R Documentation

Subdivides Sequences into n Bins

Description

Preprocessing function for SPMA, divides transcript sequences into n bins.

Usage

subdivide_data(sorted_transcript_sequences, n_bins = 40)

Arguments

`sorted_transcript_sequences`	character vector of named sequences (names are usually RefSeq identifiers and sequence region labels, e.g., "NM_1_DUMMY\|3UTR"). It is important that the sequences are already sorted by fold change, signal-to-noise ratio or any other meaningful measure.
`n_bins`	specifies the number of bins in which the sequences will be divided, valid values are between 7 and 100

Value

An array of n_bins length, containing the binned sequences

Examples

# toy example
toy_seqs <- c(
  "CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU", "UCAUUUUAUUAAA",
  "AAUUGGUGUCUGGAUACUUCCCUGUACAU", "AUCAAAUUA", "AGAU", "GACACUUAAAGAUCCU",
  "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA", "AUAGAC", "AGUUC", "CCAGUAA"
)
# names are used as keys in the hash table (cached version only)
# ideally sequence identifiers (e.g., RefSeq ids) and
# sequence region labels (e.g., 3UTR for 3'-UTR)
names(toy_seqs) <- c(
  "NM_1_DUMMY|3UTR", "NM_2_DUMMY|3UTR", "NM_3_DUMMY|3UTR",
  "NM_4_DUMMY|3UTR", "NM_5_DUMMY|3UTR", "NM_6_DUMMY|3UTR",
  "NM_7_DUMMY|3UTR",
  "NM_8_DUMMY|3UTR", "NM_9_DUMMY|3UTR", "NM_10_DUMMY|3UTR",
  "NM_11_DUMMY|3UTR",
  "NM_12_DUMMY|3UTR", "NM_13_DUMMY|3UTR", "NM_14_DUMMY|3UTR"
)

foreground_sets <- subdivide_data(toy_seqs, n_bins = 7)

# example data set
background_df <- transite:::ge$background_df
# sort sequences by signal-to-noise ratio
background_df <- dplyr::arrange(background_df, value)
# character vector of named sequences
background_seqs <- background_df$seq
names(background_seqs) <- paste0(background_df$refseq, "|",
  background_df$seq_type)

foreground_sets <- subdivide_data(background_seqs)

kkrismer/transite documentation built on July 13, 2024, 8:01 a.m.