PepMapViz (version 1.1.0)

peptide_quantification: Peptide Quantification

Description

Peptide Quantification

Usage

peptide_quantification(
  whole_seq,
  matching_result,
  matching_columns,
  distinct_columns,
  quantify_method,
  area_column = NULL,
  with_PTM = FALSE,
  reps = FALSE
)

Value

Returns a dataframe containing the calculated PSM or Area for each record in 'whole_seq'.

Arguments

whole_seq

A dataframe holding whole sequence information. 'Region_Sequence' column is required for the sequence information. Change the column name if it is different than 'Region_Sequence'.

matching_result

The dataframe that contains the matched results and PTM information.

matching_columns

Vector of column names that should match between each row of 'whole_seq' and the 'matching_result' dataframe.

distinct_columns

Vector of column names that should be used to calculate PSM or Area separately for each unique combination of these columns.

quantify_method

A string indicating the quantification method. It can be either "PSM" or "Area".

area_column

The name of the column in 'matching_result' that contains the area/intensity information. Required if quantify_method is "Area".

with_PTM

A boolean parameter indicating whether PTM should be considered during calculation. Default is FALSE.

reps

A boolean parameter indicating whether the area/intensity should be divided by the number of replicates. Default is FALSE.

Examples

whole_seq <- data.frame(
  Region_Sequence = c(
    "XYZAAA",
    "XYZCCC",
    "XYZBBB",
    "XYZDDD",
    "XYZAAB",
    "XYZCCD",
    "XYZBBB",
    "XYZDDD",
    "XYZAAA",
    "XYZCCC",
    "XYZBBB",
    "XYZDDD",
    "XYZAAB",
    "XYZCCD",
    "XYZBBB",
    "XYZDDD"
  ),
  Condition_1 = c(
    "Drug1",
    "Drug1",
    "Drug2",
    "Drug2",
    "Drug1",
    "Drug1",
    "Drug2",
    "Drug2",
    "Drug1",
    "Drug1",
    "Drug2",
    "Drug2",
    "Drug1",
    "Drug1",
    "Drug2",
    "Drug2"
  ),
  Condition_2 = c(
    "Donor1",
    "Donor1",
    "Donor1",
    "Donor1",
    "Donor1",
    "Donor1",
    "Donor1",
    "Donor1",
    "Donor2",
    "Donor2",
    "Donor2",
    "Donor2",
    "Donor2",
    "Donor2",
    "Donor2",
    "Donor2"
  ),
  Region_1 = c(
    "VH",
    "VL",
    "VH",
    "VL",
    "VH",
    "VL",
    "VH",
    "VL",
    "VH",
    "VL",
    "VH",
    "VL",
    "VH",
    "VL",
    "VH",
    "VL"
  ),
  Region_2 = c(
    "Arm_1",
    "Arm_1",
    "Arm_1",
    "Arm_1",
    "Arm_2",
    "Arm_2",
    "Arm_2",
    "Arm_2",
    "Arm_1",
    "Arm_1",
    "Arm_1",
    "Arm_1",
    "Arm_2",
    "Arm_2",
    "Arm_2",
    "Arm_2"
  )
)
matching_result <- data.frame(
  Sequence = c("AAA", "DDD", "DDD"),
  Condition_1 = c("Drug1", "Drug2", "Drug2"),
  Condition_2 = c("Donor1", "Donor2", "Donor2"),
  Region_1 = c("VH", "VL", "VL"),
  Region_2 = c("Arm_1", "Arm_2", "Arm_2"),
  start_position = c(4, 4, 4),
  end_position = c(6, 6, 6),
  PTM_position = c(NA, 2, 0),
  PTM_type = c(NA, "O", "C"),
  Area = c(100, 200, 200),
  reps = c(1, 2, 2)
)
matching_columns <- c("Condition_1", "Region_2")
area_column <- "Area"
data_with_quantification <- peptide_quantification(
  whole_seq,
  matching_result,
  matching_columns,
  distinct_columns = c("Condition_2", "Region_1"),
  quantify_method = "Area",
  area_column = area_column,
  with_PTM = TRUE,
  reps = TRUE
)