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Validate sequence window alignment

Source: R/feature_preparation.R
validate_sequence_window.Rd

Filters phosphosite data to keep only rows where the central residue of the SequenceWindow matches the reported modified amino acid (modAA).

Usage

validate_sequence_window(
  data,
  seq_col = "SequenceWindow",
  mod_col = "modAA",
  center_pos = 8L
)

Arguments

data

Data frame with PTM results containing SequenceWindow and modAA columns

seq_col

Character. Name of sequence window column. Default "SequenceWindow"

mod_col

Character. Name of modified amino acid column. Default "modAA"

center_pos

Integer. Position of the central residue (1-indexed). Default 8

Value

Filtered data frame with only valid sequence windows

Details

Sequence windows should be centered on the modified residue. This function validates that the character at the center position matches the reported modification site. Both are converted to uppercase for comparison.

Examples

data <- data.frame(
  SequenceWindow = c("AAASAAAA", "BBBSBBB", "CCCACCC"),
  modAA = c("S", "S", "S")
)
validate_sequence_window(data)
#> [1] SequenceWindow modAA         
#> <0 rows> (or 0-length row.names)
# Only first two rows kept (center matches S)