Generate statistics based on sequence matches and DE data

Usage

SeedMatchReport(
  res,
  seqs,
  guide.seq,
  group.name = "SeedMatchReport",
  indel.bool = TRUE,
  allow_wobbles = FALSE,
  log2fc.cut = -0.7655347,
  padj.cut = 0.05,
  seed.edit.distances = 0,
  fixed = T
)

Arguments

res: A data.frame of DESeq2 results
seqs: A Biostrings::DNAStringSet of sequences to search
guide.seq: Input RNA sequence as a character vector
group.name: The group name to use for labeling rows
indel.bool: Boolean in long format (TRUE, FALSE) for whether to include indels.
allow_wobbles: Whether to allow G:U wobbles in the search.
log2fc.cut: Log2(FC) threshold for considering a gene an off-target.
padj.cut: Adjust p-value threshold
seed.edit.distances: An integer value indicating allowed edit distance for seed searches.
fixed: Whether IUPAC values need to match for ambiguous chracters.

Value

A list containing: report: a data.frame of results table: a gt::gt table of results matches: A data.frame of matches

Examples

if (FALSE) { # interactive()
#' guide.seq = "UUAUAGAGCAAGAACACUGUUUU"

anno.db = load_annotations("rnor7")

# Load test data
get_example_data("sirna")

sirna.data = load_example_data("sirna")

res <- sirna.data$Schlegel_2022_Ttr_D1_30mkg

# Filter DESeq2 results for SeedMatchR
res = filter_res(res, fdr.cutoff=1, fc.cutoff=0, rm.na.log2fc = TRUE)

SeedMatchReport(res, anno.db$seqs, anno.db$gtf, guide.seq, "si-Ttr")
}