In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

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Overview

Certain functions have been included in pmartR to simplify the user's experience by allowing them to retrieve information stored in attributes of the omicsData object. We'll demonstrate these functions with some of the example omicsData objects from the pmartRdata package.

library(pmartR)
library(pmartRdata)
mypro <- pro_object
mymetab <- metab_object
mynmr <- nmr_identified_object

Related to Data Structure or Setup

• get_data_class() - Returns data_class attribute from statRes or trellData object, inherited from the omicsData used in imd_anova() or format_data()

# get a statRes object using the proData object
mypro <- group_designation(omicsData = mypro, main_effects = "Phenotype")
myfilter <- imdanova_filter(omicsData = mypro)
mypro <- applyFilt(filter_object = myfilter, omicsData = mypro, min_nonmiss_anova = 2, min_nonmiss_gtest = 3)
mystats <- imd_anova(omicsData = mypro, test_method = "combined")

get_data_class(mystats)

• get_data_info() - Returns a list containing the data scale, normalization information, number of unique entries in e_data, number of missing observations in e_data, proportion of missing observations in e_data, number of samples, and data type

get_data_info(omicsData = mypro)

• get_data_scale() - Returns current data scale which may be different from the original data scale (if edata_transform() was used)

get_data_scale(omicsObject = mypro)
get_data_scale(omicsObject = mymetab)
get_data_scale(omicsObject = mynmr)

• get_data_scale_orig() - Retrieves the character string indicating the scale the data was originally on when the omicsData object was created

get_data_scale_orig(omicsObject = mypro)
get_data_scale_orig(omicsObject = mymetab)
get_data_scale_orig(omicsObject = mynmr)

• get_edata_cname() - Returns the name of the column in e_data that contains the biomolecule IDs

get_edata_cname(omicsObject = mypro)
get_edata_cname(omicsObject = mymetab)
get_edata_cname(omicsObject = mynmr)

• get_emeta_cname() - Returns the name of the column in e_meta that contains the mapping to biomolecules in e_data

get_emeta_cname(omicsObject = mypro)
get_emeta_cname(omicsObject = mymetab)
get_emeta_cname(omicsObject = mynmr)

• get_fdata_cname() - Returns the name of the column in f_data that contains the names of the samples

get_fdata_cname(omicsObject = mypro)
get_fdata_cname(omicsObject = mymetab)
get_fdata_cname(omicsObject = mynmr)

• get_group_DF() - A data.frame with columns for sample ID and group. If two main effects are provided, the original main effect levels for each sample are returned as the third and fourth columns of the data frame. Additionally, the covariates provided will be listed as attributes of this data frame. For both mymetab and mynmr, we have not designated groups yet so the results are NULL.

get_group_DF(omicsData = mypro)
get_group_DF(omicsData = mymetab)
get_group_DF(omicsData = mynmr)

• get_group_table() - This function returns a table with number of samples per group

get_group_table(omicsObject = mypro)

• get_isobaric_info() - A list containing the following six elements: exp_cname, channel_cname, refpool_channel, refpool_cname, refpool_notation, and norm_info (list containing a single logical element that indicates whether the data have been normalized to a reference pool

myiso <- edata_transform(omicsData = isobaric_object, data_scale = "log2")
myiso_normalized <- normalize_isobaric(
  omicsData = myiso,
  exp_cname = "Plex",
  apply_norm = TRUE,
  refpool_cname = "Virus",
  refpool_notation = "Pool"
)
get_isobaric_info(omicsData = myiso_normalized)

• get_meta_info() - Retrieves the values in the meta_info attribute from an omicsData object

get_meta_info(omicsData = mynmr)

• get_nmr_info() - A list containing the following three elements: metabolite_name, sample_property_cname, and norm_info (list containing two logical elements that indicate i) whether the data have been normalized to a spiked in metabolite or to a property taking sample-specific values and ii) whether the data have been back transformed so the values are on a similar scale to the raw values before normalization.

get_nmr_info(omicsData = mynmr)

mynmr <- edata_transform(
  omicsData = nmr_identified_object,
  data_scale = "log2"
)

# Normalization using a "spiked in" metabolite
nmr_norm <- normalize_nmr(
  omicsData = mynmr, apply_norm = TRUE,
  metabolite_name = "unkm1.53",
  backtransform = TRUE
)
get_nmr_info(omicsData = nmr_norm)

# Normalization using a sample property
nmr_norm <- normalize_nmr(
  omicsData = mynmr, apply_norm = TRUE,
  sample_property_cname = "Concentration",
  backtransform = TRUE
)
get_nmr_info(omicsData = nmr_norm)

Related to Filters

• get_filters() - A list containing filter class objects. Each element in this list corresponds to a filter applied to the data, and filters are listed in the order they were applied.

get_filters(omicsData = mypro)

Related to Normalization

• get_data_norm() - Returns the norm_info element of the data_info attribute indicating whether the data have been normalized

get_data_norm(omicsObject = mypro)
get_data_norm(omicsObject = mymetab)
get_data_norm(omicsObject = mynmr)

• get_isobaric_norm() - A logical value indicating whether the data have been isobaric normalized

get_isobaric_norm(myiso)
get_isobaric_norm(myiso_normalized)

• get_nmr_norm() - A logical value indicating whether the data have been NMR normalized

get_nmr_norm(omicsData = mynmr)
get_nmr_norm(omicsData = nmr_norm)

Related to Statistical Comparisons

• get_comparisons() - Returns a data frame with comparisons and their indices

imd_anova_res <- imd_anova(
  omicsData = mypro,
  test_method = "comb",
  pval_adjust_a_multcomp = "bon",
  pval_adjust_g_multcomp = "bon"
)

get_comparisons(compObj = imd_anova_res)

References

pmartR/pmartR documentation built on May 5, 2024, 12:03 a.m.