Study_abstract-class: A Reference Class to represent a multi-omic study.
In fchuffar/epimedtools: Useful Tools Allowing Multi-Omics Analysis

Study_abstract-class

R Documentation

A Reference Class to represent a multi-omic study.

Description

This class allow to manipulate useful concepts involved in a multi-omics study. It an abstract class.

Fields

platform: The Table version of the GEO platform description.
platform_filenames: A character string that describes the platform file name.
cache_filename: A character string that describes the study cache file name.
gset: The GEO set of data as it is return by getGEO.
gse: A character string that describes the GEO accession number.
series_matrix_filename: A character string that describes the GEO serie matrix family file name.
data: A matris of experiemental data. Each column is a sample, named by it's sample name, and each row is a probes.
platform_name: A character string that describes the platform used to perform.
exp_grp: A data.frame that describe the experimental grouping. Each line is a sample.
cel_filedirs: A character string that describes the directory taht contain associated cel files.

Methods

do_anova(probe_names, samples_names, exp_grp_key): Performs anova test for a given 'probe_name' and a given 'exp_grp_key'.
do_fast_fc(probe_names, ctrl_key, case_key, ctrl_fctr, case_fctr): Perform a Mann-Whitney test to detect shifted ('two.sided' 'less' or 'greater') expression groups for a given 'probe_name' and a given 'exp_grp_key'.
do_gm2sd_analysis(probe_names, ctrl_key, case_key, ctrl_fctr, case_fctr, ctrl_thres_func = m2sd, case_value_func = mean, comp_func = get("<"), nb_perm = 100, MONITORED = FALSE): Performs permutation test to detect right shifted expression groups for two given groups.
do_mw_test(probe_names, ctrl_key, case_key, ctrl_fctr, case_fctr, ...): Perform a Mann-Whitney test to detect shifted ('two.sided', 'less' or 'greater') expression groups for a given 'probe_name' and a given 'exp_grp_key'.
get_cel_files(dest_dir = "data", ...): Retrieve .CEL.gz from NCBI GEO eweb site
get_gset(CACHE = TRUE, MEMOISE = FALSE, dest_dir = "data"): Computes (if not yet done) and returns the gset field.
get_platform(CACHE = FALSE, MEMOISE = TRUE, dest_dir = "data/platforms"): Computes if not and returns the platform field.
get_probe_gene_tab(genes, DEEP_SEARCH = FALSE, pf_col_name = "Gene Symbol", col_delimiter = "[ /]+", ...): Build a gene / probe table from a gene list.
get_ratio(ctrl_sample_names, method = "mean", ...): Normalize data accross probes using method *method* according to a reference poulation describe by *ctrl_sample_names* its sample names vector.
gs_to_probe(gene, ALL_PF_COL = FALSE, pf_col_name = "Gene Symbol", col_delimiter = "[ /]+", ...): Return probes name for a given gene.
initialize(cfn, MEMOISATION = FALSE): Constructor.
plot_boxplot(probe_name, exp_grp_key, gene_name, ylim, las = 2, col = "grey", border = "black", bp_function_name = "boxplot", ...): Draw the box plot for a given 'probe_name' and a given 'exp_grp_key'.
plot_boxplot2(probe_names, ctrl_key, case_key, ctrl_fctr, case_fctr, ylim, las = 2, col = "grey", border = "black", bp_function_name = "boxplot"): Draw the box plot for a given 'probe_name' and a given 'exp_grp_key'.
plot_qc(method = "boxplot", ...): Plot the quality control of the study.
pretreat_before_a_test(probe_names, ctrl_key, case_key, ctrl_fctr, case_fctr, two_grp_test_func, for_each_line_process_groups_func = "for_each_line_process_groups_two_by_two_func", ...): Perform a pretreatment on data, according to 'probe_names' and 'exp_grp' keys and factors, before processing the dataset.
save(cache_filename, FORCE = FALSE): Writes the study on the disk.
set_data(hook, method_to_read_cel_files, ...): Set the data field and update experiment grouping.