lFC_in_time: Plot fold change in time

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

Description

lFC_in_time function could be used to plot fold change in time for chosen genes or miRNAs by gene symbol or MIMAT ids respectively.

Usage

lFC_in_time(genes_to_valid, dane_ranking_z_scores, scale = "linear",
  miRNA = FALSE)

Arguments

genes_to_valid	Character vector with gene symbols or MIMAT ids (for miRNA) which fold change in time should be plotted.
dane_ranking_z_scores	A list - output of create_ranking function.
scale	A character indicating the scale of plot. Could be 'linear' for fold change or 'log' for logarithmic fold change. Default value is 'linear'.
miRNA	Logical indicating if plot is created for gene or miRNA ranking.

Value

Function returns a ggplot object which could be plotted with plot function as in the examples.

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)

# plot fold change in time for some genes
genes_to_plot = c('GAPDH', 'ACTB', 'LYPLA2', 'B2M', 'TP53')
genes_FC_in_time = lFC_in_time(genes_to_plot, gene_ranking)

##### Create stability ranking for miRNAs

# download data from ArrayExpress database
datamiRNA = downloadAE("E-MTAB-5197", "/home/emarek/")

# prepare table as shown in details load_miRNA help page
path_to_table = system.file("inst/extdata", "miRNA_ex1.rds", package = "FindReference")
my_table = readRDS(path_to_table)

# load data
loaded_data = load_miRNA(my_table, datamiRNA[[1]]$path)

# normalize and annotate data
norm_data = norm_and_annot_miRNA(loaded_data)

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

# create ranking
miRNA_ranking = create_ranking(no_rep$noRepData, no_rep$uniqSamples, miRNA = TRUE)

# plot fold change in time for the most stable miRNAs
miRNA_to_plot = miRNA_ranking$miRNA_ranking[1:9, 'ID']
genes_FC_in_time = lFC_in_time(miRNA_to_plot, miRNA_ranking, scale = 'linear', miRNA = TRUE)

## End(Not run)

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