hpepLFQ: Spreads Mzion peptide numbers.

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

Spreads Mzion peptide numbers.

Description

No aggregation of data at the same TMT_Set but different LCMS_Injs.

Usage

hpepLFQ(
  filelist,
  basenames,
  set_idxes,
  injn_idxes,
  are_refs,
  are_smpls,
  dfs = NULL,
  df_sps = NULL,
  prot_spec_counts = NULL,
  use_spec_counts = FALSE,
  dat_dir = NULL,
  path_ms1 = NULL,
  ms1files = NULL,
  temp_dir = NULL,
  rt_tol = 30,
  mbr_ret_tol = 30,
  sp_centers_only = FALSE,
  imp_refs = FALSE,
  group_psm_by = "pep_seq_modz",
  group_pep_by = "gene",
  lfq_mbr = FALSE,
  rt_step = 0.005,
  new_na_species = ".other",
  max_mbr_fold = 20
)

Arguments

filelist	The name of peptide files (TMTset1_LCMSinj1_Peptide_N.txt) with prepending path.
basenames	The basenames corresponding to filelist.
set_idxes	The TMT_Set indexes corresponding to basenames.
injn_idxes	The LCMS_Injection indexes corresponding to basenames.
are_refs	A logical vector corresponding to basenames, indicating the reference status.
are_smpls	A logical vector corresponding to basenames, indicating the sample status.
dfs	Lists of peptide tables in correspondence to filelist.
df_sps	A look-up table between peptide sequences and species.
prot_spec_counts	A data frame of protein spectrum counts.
use_spec_counts	Logical; use spectrum counts instead of intensities or not.
dat_dir	The working directory.
path_ms1	The path to MS1 data files.
ms1files	The names of MS1 data files.
temp_dir	The path to temporary files.
rt_tol	Error tolerance in retention times.
mbr_ret_tol	The tolerance in MBR retention time in seconds.
sp_centers_only	Logical; for a side-effect to return only the values of species centers.
imp_refs	Logical; impute missing references or not.
group_psm_by	Group PSMs by.
group_pep_by	Group peptides by.
lfq_mbr	Logical; if TRUE, performs match-between-run (MBR) with Mzion LFQ data. Also requires ms1full_[rawfile].rds at the same file-folder level of psmQ[...].txt.
rt_step	The step size in binning retention times.
new_na_species	A replace value for NA species.
max_mbr_fold	Not used. The maximum absolute fold change in MBR.

Details

Spreads fields of numeric values: sd_log2_R, log2_R, log2_R, I, N_I by TMT sets.

Also works for LFQ as each sample corresponds to a TMT set.

For single SILAC sample, the values of log2Ratios spreads into MULTIPLE columns of heavy, light etc. Despite, log2Ratios remains NA, just like regular single-sample LFQ. The log2Ratios will be later calculated with calcLFQPepNums that are based on intensity values.

qzhang503/proteoQ documentation built on Feb. 27, 2025, 8:34 a.m.