plot_3_pep_trends_NOfile: Plot peptide trends

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

Plot peptide trends

Description

Plot Raw, Normalized and Normalized & Imputed peptide trends for a protein

Usage

plot_3_pep_trends_NOfile(
  mm,
  prot.info,
  sorted_norm_m,
  sorted_prot.info,
  imp_mm,
  imp_prot.info,
  prot_to_plot,
  prot_to_plot_col,
  gene_name,
  gene_name_col,
  mylabs
)

Arguments

mm	matrix of raw intensities
prot.info	metadata for the intensities in mm
sorted_norm_m	normalized intensities, possibly fewer than in mm due to filtering out peptides with fewer than one observation per treatment group
sorted_prot.info	metadata for the intensities in sorted_norm_m
imp_mm	imputed intensities (post normalization)
imp_prot.info	metadata for the imputed intensities in imp_mm
prot_to_plot	protein ID to plot
prot_to_plot_col	protein ID column index
gene_name	gene ID to plot
gene_name_col	gene ID to plot column index
mylabs	sample labels to be plotted on x-axis

Value

Nil

Examples

data("hs_peptides") # loads variable hs_peptides
intsCols = 8:13 # column indeces that contain intensities
m_logInts = make_intencities(hs_peptides, intsCols)
# replace 0's with NA's as NA's are more appropriate
# for anlysis and log2 transform
m_logInts = convert_log2(m_logInts)
# column indices that contain metadata such as protein IDs and sequences
metaCols = 1:7
m_prot.info = make_meta(hs_peptides, metaCols)
grps = as.factor(c('CG','CG','CG', 'mCG','mCG','mCG'))

set.seed(135)
hs_m_ints_eig1 = eig_norm1(m=m_logInts,treatment=grps,prot.info=m_prot.info)
hs_m_ints_eig1$h.c = 2 # looks like there are 2 bias trends at least
hs_m_ints_norm = eig_norm2(rv=hs_m_ints_eig1)
hs_prot.info = hs_m_ints_norm$normalized[,metaCols]
hs_norm_m =  hs_m_ints_norm$normalized[,intsCols]

set.seed(125)
imp_hs = MBimpute(hs_norm_m, grps, prot.info=hs_prot.info,
                  pr_ppos=3, my.pi=0.05, compute_pi=FALSE)
mylabs = c( 'CG','CG','CG', 'mCG','mCG','mCG')
prot_to_plot = 'Prot32' # 43
gene_to_plot = 'Gene32'
plot_3_pep_trends_NOfile(as.matrix(hs_m_ints_eig1$m),
                         hs_m_ints_eig1$prot.info,
                         as.matrix(hs_norm_m),
                         hs_prot.info,
                         imp_hs$y_imputed,
                         imp_hs$imp_prot.info,
                         prot_to_plot, 3,
                         gene_to_plot, 4, mylabs)

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