inst/extdata/examples/normPSM_.R

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

\donttest{
# ===================================
# PSM normalization
# ===================================

## !!!require the brief working example in `?load_expts`

## additional examples
# Mascot
normPSM(
  group_psm_by = pep_seq_mod,
  group_pep_by = prot_acc,
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  
  # variable argument statement(s)
  filter_psms_at = exprs(pep_expect <= .1),
  filter_psms_more = exprs(pep_rank == 1, pep_exp_z > 1),
)

# MaxQuant
normPSM(
  group_psm_by = pep_seq_mod,
  group_pep_by = prot_acc,
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  corrected_int = TRUE,
  rm_reverses = TRUE,
  
  # vararg statement(s)
  filter_psms_at = exprs(PEP <= 0.1),
)

# MSFragger
normPSM(
  group_psm_by = pep_seq_mod,
  group_pep_by = prot_acc,
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),

  # vararg statement(s)
  filter_psms_at = exprs(Hyperscore >= 10),
)

# Spectrum Mill
normPSM(
  group_psm_by = pep_seq_mod,
  group_pep_by = prot_acc,
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  
  # vararg statement(s)
  filter_psms_at = exprs(score >= 10),
)

###############################################
## Custom entrez lookups
#  (1) can overwrite the `proteoQ` default for 
#      species in "human", "mouse" and "rat"
#  (2) and are required for `other` species
###############################################
# see also `?Uni2Entrez` or `?Ref2Entrez` for more examples
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("org.Hs.eg.db")
BiocManager::install("org.Mm.eg.db")

library(org.Hs.eg.db)
library(org.Mm.eg.db)

library(proteoQ)
Ref2Entrez(species = human)
Ref2Entrez(species = mouse)

# see also Uni2Entrez(...) for Uniprot to Entrez lookups

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"),
)


## Not run: 
# wrong fasta 
normPSM(
  fasta = "~/proteoQ/dbs/fasta/wrong.fasta",
)

# no mouse entry annotation
normPSM(
  fasta = "~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
)

# bad vararg statement
normPSM(
  fasta = c("~/proteoQ/dbs/fasta/refseq/refseq_hs_2013_07.fasta",
            "~/proteoQ/dbs/fasta/refseq/refseq_mm_2013_07.fasta"),
  filter_psms_at = exprs(column_key_not_in_psm_tables <= .1),
)
## End(Not run)
}