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benchmark_lfqbench_2to1_precursor.R
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# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
rm(list = ls())
library(LFQbench)
library(readr)
library(dplyr)
library(stringr)
library(tidyr)
my_process_1 <- function(input_path, tool, annotation2_path, is_spectronaut) {
if (is_spectronaut) {
annotation2 <- read_tsv(annotation2_path, col_select = c("PG.ProteinGroups", "PEP.StrippedSequence", "EG.ModifiedSequence", "FG.Charge")) %>%
rename(Protein.Group = PG.ProteinGroups, Stripped.Sequence = PEP.StrippedSequence) %>%
mutate(Precursor.Id = paste0(EG.ModifiedSequence, FG.Charge))
} else {
annotation2 <- read_tsv(annotation2_path, col_select = c("Protein.Group", "Stripped.Sequence", "Precursor.Id"))
}
annotation2 <- annotation2 %>%
distinct(Precursor.Id, .keep_all = TRUE) %>%
separate(col = Protein.Group, into = "Entry", sep = ";", remove = TRUE, extra = "drop") %>%
inner_join(annotation)
input_table <- read_tsv(file = input_path)
colnames(input_table)[2:length(colnames(input_table))] <- gsub("$", " intensity", colnames(input_table)[2:length(colnames(input_table))])
input_table <- input_table %>%
rename(Precursor.Id = `...1`) %>%
select(c("Precursor.Id", contains("1-6"), contains("1-12"))) %>%
inner_join(annotation2) %>%
filter(!(Stripped.Sequence %in% human_ecoli_overlap_peptide$V1)) %>%
mutate(Protein = paste0("sp|", Precursor.Id, "|", `Entry name`))
colnames(input_table) <- sub("-", "_", colnames(input_table))
write_tsv(input_table, str_c(srcDir, str_c(tool, ".tsv")))
}
setwd("G:\\Dropbox\\papers_Fengchao\\msfragger_dia\\script\\results\\benchmark\\")
annotation <- read_tsv("G:\\Dropbox\\papers_Fengchao\\msfragger_dia\\script\\code\\MSFragger-DIA-manuscript\\uniprot.tab", col_select = c("Entry", "Entry name"))
human_ecoli_overlap_peptide <- read.delim("human_ecoli_overlap_peptides.txt", header = FALSE, sep = "\t")
srcDir <- "./lfqbench_benchmark_2to1_precursor/"
unlink(srcDir, recursive = TRUE)
mkdir(srcDir)
my_process_1("spectronaut\\14\\precursor_maxlfq.tsv", "my_spectronaut_14", "spectronaut\\14\\20230227_181426_directDIA_LymphEcoli_Report.tsv", TRUE)
my_process_1("spectronaut\\17\\precursor_maxlfq.tsv", "my_spectronaut_17", "spectronaut\\17\\20230227_180032_SN17_RealDilutionSeries_Report.tsv", TRUE)
my_process_1("diann\\precursor_maxlfq.tsv", "diann", "diann\\diann-output.tsv", FALSE)
my_process_1("msfraggerdia\\precursor_maxlfq.tsv", "msfraggerdia", "msfraggerdia\\diann-output.tsv", FALSE)
my_process_1("msfraggerdiadda\\precursor_maxlfq.tsv", "msfragger_hybrid", "msfraggerdiadda\\diann-output.tsv", FALSE)
sampleComposition <- data.frame(
species = c("HUMAN", "ECOLI"),
A = c(1, 2),
B = c(1, 1)
)
dataSets <- data.frame(
"HYE124" = c("Lymph_Ecoli_1_6_011",
"Lymph_Ecoli_1_6_012",
"Lymph_Ecoli_1_6_013",
"Lymph_Ecoli_1_6_026",
"Lymph_Ecoli_1_6_027",
"Lymph_Ecoli_1_6_028",
"Lymph_Ecoli_1_6_039",
"Lymph_Ecoli_1_6_041",
"Lymph_Ecoli_1_6_042",
"Lymph_Ecoli_1_6_053",
"Lymph_Ecoli_1_6_054",
"Lymph_Ecoli_1_6_055",
"Lymph_Ecoli_1_6_070",
"Lymph_Ecoli_1_6_071",
"Lymph_Ecoli_1_6_072",
"Lymph_Ecoli_1_6_074",
"Lymph_Ecoli_1_6_093",
"Lymph_Ecoli_1_6_094",
"Lymph_Ecoli_1_6_095",
"Lymph_Ecoli_1_6_096",
"Lymph_Ecoli_1_6_097",
"Lymph_Ecoli_1_6_105",
"Lymph_Ecoli_1_6_106",
"Lymph_Ecoli_1_12_008",
"Lymph_Ecoli_1_12_009",
"Lymph_Ecoli_1_12_010",
"Lymph_Ecoli_1_12_022",
"Lymph_Ecoli_1_12_023",
"Lymph_Ecoli_1_12_024",
"Lymph_Ecoli_1_12_036",
"Lymph_Ecoli_1_12_037",
"Lymph_Ecoli_1_12_038",
"Lymph_Ecoli_1_12_050",
"Lymph_Ecoli_1_12_051",
"Lymph_Ecoli_1_12_052",
"Lymph_Ecoli_1_12_066",
"Lymph_Ecoli_1_12_067",
"Lymph_Ecoli_1_12_068",
"Lymph_Ecoli_1_12_069",
"Lymph_Ecoli_1_12_088",
"Lymph_Ecoli_1_12_089",
"Lymph_Ecoli_1_12_090",
"Lymph_Ecoli_1_12_091",
"Lymph_Ecoli_1_12_092",
"Lymph_Ecoli_1_12_103",
"Lymph_Ecoli_1_12_104"
),
row.names = c("A1", "A2", "A3", "A4", "A5", "A6", "A7", "A8", "A9", "A10", "A11", "A12", "A13", "A14", "A15", "A16", "A17", "A18", "A19", "A20", "A21", "A22", "A23", "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15", "B16", "B17", "B18", "B19", "B20", "B21", "B22", "B23")
)
speciesTags <- list(
HUMAN = "_HUMAN",
ECOLI = "_ECOLI"
)
LFQbench.initConfiguration(
SampleComposition = sampleComposition
)
FSWE.initConfiguration(
injectionNames = dataSets,
speciesTags = speciesTags
)
LFQbench.setDataRootFolder(
rootFolder = srcDir,
createSubfolders = FALSE
)
FSWE.addSoftwareConfiguration(
softwareName = "my_spectronaut",
input_format = "wide",
input.extension = "*.tsv$",
nastrings = "NA",
protein_input = TRUE,
quantitative.var = "intensity",
quantitative.var.tag = "intensity",
protein.var = "Protein",
)
FSWE.addSoftwareConfiguration(
softwareName = "diann",
input_format = "wide",
input.extension = "*.tsv$",
nastrings = "NA",
protein_input = TRUE,
quantitative.var = "intensity",
quantitative.var.tag = "intensity",
protein.var = "Protein",
)
FSWE.addSoftwareConfiguration(
softwareName = "msfraggerdia",
input_format = "wide",
input.extension = "*.tsv$",
nastrings = "NA",
protein_input = TRUE,
quantitative.var = "intensity",
quantitative.var.tag = "intensity",
protein.var = "Protein",
)
FSWE.addSoftwareConfiguration(
softwareName = "msfragger_hybrid",
input_format = "wide",
input.extension = "*.tsv$",
nastrings = "NA",
protein_input = TRUE,
quantitative.var = "intensity",
quantitative.var.tag = "intensity",
protein.var = "Protein",
)
inputFiles <- list.files(
path = LFQbench.Config$DataRootFolder,
pattern = ".+\\.tsv"
)
nix <- sapply(
inputFiles,
FSWE.generateReports,
softwareSource = "guess",
keep_original_names = T,
singleHits = F,
plotHistogram = T,
plotHistNAs = T,
reportSequences = F
)
# some configuration changes for beautifying plots
LFQbench.changeConfiguration(
PlotPointSize = 0.5,
LogRatioPlotRange = c(-5, 5),
LogRatioValidityRangeSDFactor = 50
)
# run batch analysis and keep result set
res <- LFQbench.batchProcessRootFolder()