Uni2Entrez: Map UniProt accessions to Entrez IDs

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Map UniProt accessions to Entrez IDs

Description

Uni2Entrez prepares lookup tables between UniProt accessions and Entrez IDs for uses with normPSM and downstream gene-set analysis such as prnGSPA. The utility is optional for human, mouse and rat data. It is required for other species with prnGSPA in users' workflows. It can also be used to update and overrule the lookups for human, mouse and rat that are defaulted by proteoQ.

Ref2Entrez prepares lookup tables between RefSeq accessions and Entrez IDs and gene names for uses with normPSM and downstream gene-set analysis such as prnGSPA. The utility is optional for human and mouse data. It is required for other species with prnGSPA in users' workflows. It can also be used to update and overrule the lookups for human and mouse that are defaulted by proteoQ.

Usage

Uni2Entrez(
  species = "human",
  abbr_species = NULL,
  filename = NULL,
  db_path = "~/proteoQ/dbs/entrez",
  overwrite = FALSE
)

Ref2Entrez(
  species = "human",
  abbr_species = NULL,
  filename = NULL,
  db_path = "~/proteoQ/dbs/entrez",
  overwrite = FALSE
)

Arguments

species	Character string; the name of a species.
abbr_species	Two-letter character string; the abbreviated name of species used with org.Xx.eg.db. The value of abbr_species will be determined automatically if the species is in one of c("human", "mouse", "rat"). Otherwise, for example, users need to provide abbr_species = Ce for fetching the org.Ce.eg.db package in the name space of proteoQ. For analysis against gene ontology and Molecular Signatures, the argument is further applied to differentiate the same biological terms under different species; e.g., GO~0072686 mitotic spindle becomes hs_GO~0072686 mitotic spindle for human and mm_GO~0072686 mitotic spindle for mouse.
filename	Character string; An output file name. At the NULL default, the name will be determined automatically at a given species; i.e., msig_hs.rds for human data. The file is saved as a .rds object for uses with prnGSPA.
db_path	Character string; the local path for database(s). The default is "~/proteoQ/dbs/entrez".
overwrite	Logical; if TRUE, overwrite the downloaded database(s). The default is FALSE.

Examples

# ===============================================
# Apply custom `human` and `mouse` Entrez lookups
# ===============================================
## A RefSeq example
# Prep I: fetch up-to-date `org.Xx.eg.db`
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
  
BiocManager::install("org.Hs.eg.db")
BiocManager::install("org.Mm.eg.db")

# Prep II: make available RefSeq Fasta(s) if not yet
library(proteoQDA)
db_path <- "~/proteoQ/dbs/fasta/refseq"
copy_refseq_hs(db_path)
copy_refseq_mm(db_path)

# Prep III: copy metadata and PSMs if not yet
dat_dir <- "~/proteoQ/custom_refseq_lookups"
copy_global_exptsmry(dat_dir)
copy_global_fracsmry(dat_dir)

# (for MaxQuant, use `copy_global_maxquant()`)
# (for Spectrum Mill, use `copy_global_sm()`)
copy_global_mascot(dat_dir)


# --- workflow begins ---
library(proteoQ)
load_expts("~/proteoQ/custom_refseq_lookups")

# prepare RefSeq-to-Entrez lookups
Ref2Entrez(species = human)
Ref2Entrez(species = mouse)

# head(readRDS(file.path("~/proteoQ/dbs/entrez/refseq_entrez_hs.rds")))
# head(readRDS(file.path("~/proteoQ/dbs/entrez/refseq_entrez_mm.rds")))

# overrule the default `Entrez` lookups with the custom databases
normPSM(
  group_psm_by = pep_seq_mod, 
  group_pep_by = gene, 
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  entrez = c("~/proteoQ/dbs/entrez/refseq_entrez_hs.rds", 
             "~/proteoQ/dbs/entrez/refseq_entrez_mm.rds"),
)


## A UniProt example
# Prep I: set up UniProt Fasta(s) if not yet
library(proteoQDA)
db_path <- "~/proteoQ/dbs/fasta/uniprot"
copy_uniprot_hs(db_path)
copy_uniprot_mm(db_path)

# Prep II: copy metadata and PSMs if not yet
dat_dir <- "~/proteoQ/custom_uniprot_lookups"
copy_global_exptsmry(dat_dir)
copy_global_fracsmry(dat_dir)

# (for Mascot, use `copy_global_mascot()`)
# (for Spectrum Mill, use `copy_global_sm()`)
copy_global_maxquant(dat_dir)

# Prep III: simulate UniProt data from RefSeq PSMs
# (for Mascot, use `simulUniprotPSM(Mascot)`)
library(proteoQ)
simulUniprotPSM(MaxQuant)


# --- workflow begins ---
library(proteoQ)
dat_dir <- "~/proteoQ/custom_uniprot_lookups"
load_expts()

# prepare UniProt-to-Entrez lookups
Uni2Entrez(species = human)
Uni2Entrez(species = mouse)

# head(readRDS(file.path("~/proteoQ/dbs/entrez/uniprot_entrez_hs.rds")))
# head(readRDS(file.path("~/proteoQ/dbs/entrez/uniprot_entrez_mm.rds")))

normPSM(
  group_psm_by = pep_seq_mod, 
  group_pep_by = gene, 
  fasta = c("~/proteoQ/dbs/fasta/uniprot/uniprot_hs_2014_07.fasta",
            "~/proteoQ/dbs/fasta/uniprot/uniprot_mm_2014_07.fasta"),
  entrez = c("~/proteoQ/dbs/entrez/uniprot_entrez_hs.rds", 
             "~/proteoQ/dbs/entrez/uniprot_entrez_mm.rds"),
)



## Not run: 
# name your `species`
Uni2Entrez(species = this_human, abbr_species = Hs, filename = my_human.rds)
Uni2Entrez(species = this_mouse, abbr_species = Mm, filename = my_mouse.rds)

# head(readRDS(file.path("~/proteoQ/dbs/entrez/my_human.rds")))
# head(readRDS(file.path("~/proteoQ/dbs/entrez/my_mouse.rds")))

# in PSM and subsequent outputs, values under column `species` 
#  will be shown as "this_human" or "this_mouse"
normPSM(
  group_psm_by = pep_seq_mod, 
  group_pep_by = gene, 
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  entrez = c("~/proteoQ/dbs/entrez/my_human.rds", 
             "~/proteoQ/dbs/entrez/my_mouse.rds"),
)  

## End(Not run)


## Not run: 
## Custom database(s) are required for workflows 
#  with species other than `human`, `mouse` and `rat`
BiocManager::install("org.Ce.eg.db")
library(org.Ce.eg.db)

library(proteoQ)
Uni2Entrez(species = "worm", abbr_species = "Ce", filename = uniprot_entrez_ce.rds)

# --- PAUSE: prepare Fasta file(s) before proceeding to `normPSM`. ---

normPSM(
  fasta = "~/proteoQ/dbs/fasta/specify_your_worm.fasta",
  entrez = c("~/proteoQ/dbs/entrez/uniprot_entrez_ce.rds"),
)

## End(Not run)


## Not run: 
# wrong `abbr_species` provided `species` other than "human", "mouse" and "rat"
Uni2Entrez(species = "my human", abbr_species = Hu, filename = my_human.rds, overwrite = TRUE)
  
# the value of `abbr_species` ignored at `species` among "human", "mouse" and "rat"
Uni2Entrez(species = human, abbr_species = ok_not_Hs, filename = my_human.rds, overwrite = TRUE)

## End(Not run)

# ===============================================
# Apply custom `human` and `mouse` Entrez lookups
# ===============================================
## A RefSeq example
# Prep I: fetch up-to-date `org.Xx.eg.db`
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
  
BiocManager::install("org.Hs.eg.db")
BiocManager::install("org.Mm.eg.db")

# Prep II: make available RefSeq Fasta(s) if not yet
library(proteoQDA)
db_path <- "~/proteoQ/dbs/fasta/refseq"
copy_refseq_hs(db_path)
copy_refseq_mm(db_path)

# Prep III: copy metadata and PSMs if not yet
dat_dir <- "~/proteoQ/custom_refseq_lookups"
copy_global_exptsmry(dat_dir)
copy_global_fracsmry(dat_dir)

# (for MaxQuant, use `copy_global_maxquant()`)
# (for Spectrum Mill, use `copy_global_sm()`)
copy_global_mascot(dat_dir)


# --- workflow begins ---
library(proteoQ)
load_expts("~/proteoQ/custom_refseq_lookups")

# prepare RefSeq-to-Entrez lookups
Ref2Entrez(species = human)
Ref2Entrez(species = mouse)

# head(readRDS(file.path("~/proteoQ/dbs/entrez/refseq_entrez_hs.rds")))
# head(readRDS(file.path("~/proteoQ/dbs/entrez/refseq_entrez_mm.rds")))

# overrule the default `Entrez` lookups with the custom databases
normPSM(
  group_psm_by = pep_seq_mod, 
  group_pep_by = gene, 
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  entrez = c("~/proteoQ/dbs/entrez/refseq_entrez_hs.rds", 
             "~/proteoQ/dbs/entrez/refseq_entrez_mm.rds"),
)


## A UniProt example
# Prep I: set up UniProt Fasta(s) if not yet
library(proteoQDA)
db_path <- "~/proteoQ/dbs/fasta/uniprot"
copy_uniprot_hs(db_path)
copy_uniprot_mm(db_path)

# Prep II: copy metadata and PSMs if not yet
dat_dir <- "~/proteoQ/custom_uniprot_lookups"
copy_global_exptsmry(dat_dir)
copy_global_fracsmry(dat_dir)

# (for Mascot, use `copy_global_mascot()`)
# (for Spectrum Mill, use `copy_global_sm()`)
copy_global_maxquant(dat_dir)

# Prep III: simulate UniProt data from RefSeq PSMs
# (for Mascot, use `simulUniprotPSM(Mascot)`)
library(proteoQ)
simulUniprotPSM(MaxQuant)


# --- workflow begins ---
library(proteoQ)
dat_dir <- "~/proteoQ/custom_uniprot_lookups"
load_expts()

# prepare UniProt-to-Entrez lookups
Uni2Entrez(species = human)
Uni2Entrez(species = mouse)

# head(readRDS(file.path("~/proteoQ/dbs/entrez/uniprot_entrez_hs.rds")))
# head(readRDS(file.path("~/proteoQ/dbs/entrez/uniprot_entrez_mm.rds")))

normPSM(
  group_psm_by = pep_seq_mod, 
  group_pep_by = gene, 
  fasta = c("~/proteoQ/dbs/fasta/uniprot/uniprot_hs_2014_07.fasta",
            "~/proteoQ/dbs/fasta/uniprot/uniprot_mm_2014_07.fasta"),
  entrez = c("~/proteoQ/dbs/entrez/uniprot_entrez_hs.rds", 
             "~/proteoQ/dbs/entrez/uniprot_entrez_mm.rds"),
)



## Not run: 
# name your `species`
Uni2Entrez(species = this_human, abbr_species = Hs, filename = my_human.rds)
Uni2Entrez(species = this_mouse, abbr_species = Mm, filename = my_mouse.rds)

# head(readRDS(file.path("~/proteoQ/dbs/entrez/my_human.rds")))
# head(readRDS(file.path("~/proteoQ/dbs/entrez/my_mouse.rds")))

# in PSM and subsequent outputs, values under column `species` 
#  will be shown as "this_human" or "this_mouse"
normPSM(
  group_psm_by = pep_seq_mod, 
  group_pep_by = gene, 
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  entrez = c("~/proteoQ/dbs/entrez/my_human.rds", 
             "~/proteoQ/dbs/entrez/my_mouse.rds"),
)  

## End(Not run)


## Not run: 
## Custom database(s) are required for workflows 
#  with species other than `human`, `mouse` and `rat`
BiocManager::install("org.Ce.eg.db")
library(org.Ce.eg.db)

library(proteoQ)
Uni2Entrez(species = "worm", abbr_species = "Ce", filename = uniprot_entrez_ce.rds)

# --- PAUSE: prepare Fasta file(s) before proceeding to `normPSM`. ---

normPSM(
  fasta = "~/proteoQ/dbs/fasta/specify_your_worm.fasta",
  entrez = c("~/proteoQ/dbs/entrez/uniprot_entrez_ce.rds"),
)

## End(Not run)


## Not run: 
# wrong `abbr_species` provided `species` other than "human", "mouse" and "rat"
Uni2Entrez(species = "my human", abbr_species = Hu, filename = my_human.rds, overwrite = TRUE)
  
# the value of `abbr_species` ignored at `species` among "human", "mouse" and "rat"
Uni2Entrez(species = human, abbr_species = ok_not_Hs, filename = my_human.rds, overwrite = TRUE)

## End(Not run)

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.