trace_unique_common_pg {flowTraceR} | R Documentation |
Trace unique_common categorization for proteinGroup level
Description
Unique_common categorizations are analyzed on proteinGroup level
Usage
trace_unique_common_pg(
input_df1,
input_df2,
analysis_name1 = "input_df1",
analysis_name2 = "input_df2",
string_analysis = FALSE
)
Arguments
input_df1 |
A tibble with flowTraceR's unique_common categorization for the proteinGroup_precursor connection. |
input_df2 |
A tibble which is the counter part for input_df1 - which was used to generate the unique_common categorization for the proteinGroup_precursor connection. |
analysis_name1 |
String. Appended to input_df1's traceR_proteinGroups column - default is |
analysis_name2 |
String. Appended to input_df1's traceR_proteinGroups column - default is |
string_analysis |
Logical value, default is |
Details
For each submitted dataframe the unique_common proteinGroup_precursor connection is analyzed to highlight potential differences in proteinGroup denotations for common precursors.
Value
This function returns a tibble
with the following columns :
traceR_proteinGroups_input_df1 - proteinGroup denotations of input_df1 for common precursor between input_df1 and input_df2
traceR_precursor - common precursor between input_df1 and input_df2
traceR_proteinGroups_input_df2 - proteinGroup denotations of input_df2 for common precursor between input_df1 and input_df2
Author(s)
Oliver Kardell
Examples
# Load libraries
library(dplyr)
library(stringr)
library(tibble)
# DIA-NN example data
diann <- tibble::tibble(
"traceR_connected_pg_prec" = c("common_common", "common_unique",
"unique_common", "unique_common"),
"traceR_proteinGroups" = c("P02768", "P02671", "Q92496", "P04433"),
"traceR_precursor" = c("AAC(UniMod:4)LLPK1", "RLEVDIDIK2",
"EGIVEYPR2", "ASQSVSSYLAWYQQK2"),
)
# Spectronaut example data
spectronaut <- tibble::tibble(
"traceR_connected_pg_prec" = c("common_common", "common_unique",
"unique_common", "unique_common"),
"traceR_proteinGroups" = c("P02768", "P02671", "Q02985", "A0A0A0MRZ8;P04433"),
"traceR_precursor" = c("AAC(UniMod:4)LLPK1", "M(UniMod:35)KPVPDLVPGNFK2",
"EGIVEYPR2", "ASQSVSSYLAWYQQK2"),
)
# Find difference in pg denotation
# string_analysis = TRUE
resultA <- trace_unique_common_pg(input_df1 = diann,
input_df2 = spectronaut,
analysis_name1 = "DIA-NN",
analysis_name2 = "Spectronaut",
string_analysis = TRUE)
# Find difference in pg denotation
# string_analysis = FALSE
# compare with resultA
resultB <- trace_unique_common_pg(input_df1 = diann,
input_df2 = spectronaut,
analysis_name1 = "DIA-NN",
analysis_name2 = "Spectronaut",
string_analysis = FALSE)