get_presAbs_prots: Get Presence/Absence Proteins

In YuliyaLab/ProteoMM: Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

Get Presence/Absence Proteins

Description

Function get_presAbs_prots() produces a subset of protein meta data and intencities for multiple datasets pass in as a list. If a single dataset is passed in (list of length one) it will be processed in the same way as longer lists.

Usage

get_presAbs_prots(mm_list, prot.info, protnames_norm, prot_col_name)

Arguments

mm_list	list of matrices of intensities for each experiment. Dimentions: numpeptides x numsamples different for each dataset.
prot.info	list of protein and peptide metadata/mappings for each matrix in mm_list, data.frames "parallel" to matrices in mm_list.
protnames_norm	list of protein pdentifies to be used to determine peptides that will be placed into Presence/Absence analysis category due to too many missing peptides. Taken from the return value from eig_norm2().
prot_col_name	column name (string) that will be used to get ProteinIDs in the raw data matrices

Value

list of lists of length 2

intensities

list of intecities in the same order and of the same length as the number of datasets that were passed into the function

protein metadata

list of protein metadata in the same order and of the same length as the number of datasets that as were passed into the function

Examples

# Load mouse dataset
data(mm_peptides)
head(mm_peptides)
intsCols = 8:13
metaCols = 1:7 # reusing this variable
m_logInts = make_intencities(mm_peptides, intsCols)  # will reuse the name
m_prot.info = make_meta(mm_peptides, metaCols)
m_logInts = convert_log2(m_logInts)
grps = as.factor(c('CG','CG','CG', 'mCG','mCG','mCG'))
mm_m_ints_eig1 = eig_norm1(m=m_logInts,treatment=grps,prot.info=m_prot.info)
mm_m_ints_eig1$h.c # check the number of bias trends detected
mm_m_ints_norm = eig_norm2(rv=mm_m_ints_eig1)

# Load human dataset
data(hs_peptides)
head(hs_peptides)
intsCols = 8:13
metaCols = 1:7 # reusing this variable
m_logInts = make_intencities(hs_peptides, intsCols)  # will reuse the name
m_prot.info = make_meta(hs_peptides, metaCols)
m_logInts = convert_log2(m_logInts)
grps = as.factor(c('CG','CG','CG', 'mCG','mCG','mCG'))
hs_m_ints_eig1 = eig_norm1(m=m_logInts,treatment=grps,prot.info=m_prot.info)
hs_m_ints_eig1$h.c # check the number of bias trends detected
hs_m_ints_norm = eig_norm2(rv=hs_m_ints_eig1)

# Set up for presence/absence analysis
raw_list = list()
norm_imp_prot.info_list = list()
raw_list[[1]] = mm_m_ints_eig1$m
raw_list[[2]] = hs_m_ints_eig1$m
norm_imp_prot.info_list[[1]] = mm_m_ints_eig1$prot.info
norm_imp_prot.info_list[[2]] = hs_m_ints_eig1$prot.info

protnames_norm_list = list()
protnames_norm_list[[1]] = unique(mm_m_ints_norm$normalized$MatchedID)
protnames_norm_list[[2]] = unique(hs_m_ints_norm$normalized$MatchedID)

presAbs_dd = get_presAbs_prots(mm_list=raw_list,
                              prot.info=norm_imp_prot.info_list,
                              protnames_norm=protnames_norm_list,
                              prot_col_name=2)

YuliyaLab/ProteoMM documentation built on April 19, 2022, 8:12 a.m.