get_info_about_used_exp: Summarize information about experiments used to create...

In EwaMarek/FindReference: Find reference genes or miRNAs basing on microarray data.

Description

get_info_about_used_exp function summarizes conditions under which experiments used to create ranking where performed. It lists and counts used cell lines, doses and times after treatment which could be useful to see for example if some conditions where overrepresented.

Usage

get_info_about_used_exp(encoded_info, txt = TRUE, csv = TRUE,
  path = getwd())

Arguments

encoded_info	List obtained with create_ranking function.
txt	Logical indicating if .txt files with summaries should be exported into txt files. Default value is TRUE.
csv	Logical indicating if .csv files with summaries should be exported into txt files. Default value is TRUE.
path	Character indicating the directory where files with summaries should be exported. Default value is current directory.

Value

Function doesn't return a value. Summaries of used cell lines, doses and times after treating are exported into .txt, .csv files or both.

See Also

create_ranking

Examples

## Not run: 
##### Create stability ranking for genes

# download data from ArrayExpress database
to_download = c("E-GEOD-67309", "E-MTAB-966")
my_data = downloadAE(to_download, getwd())

# load data
platforms = c("Affymetrix", "Agilent")
loaded_data = load_multi_data(my_data, platforms)

# normalize and annotate
norm_data = multi_norm_and_annot(loaded_data$raw_expression_data, platforms)

# prepare tables for rep_elim function as shown in details
path_to_tables = system.file("inst/extdata", "tables_ex3.rds", package = "FindReference")
my_tables = readRDS(path_to_tables)

# eliminate replications and prepare object for create_ranking function
no_rep_data = rep_elim(norm_data, my_tables)

# create ranking
gene_ranking = create_ranking(no_rep$noRepData, no_rep$uniqSamples, miRNA = FALSE)

# summarise experimental conditions - export just .csv files in current directory
get_info_about_used_exp(gene_ranking, txt=FALSE, csv=TRUE)

## End(Not run)

EwaMarek/FindReference documentation built on May 30, 2019, 3:40 p.m.