SeqFeatR (version 0.3.3)

volcanoplot: Create volcano plot

Description

Creates a pdf output file with a volcano plot out of the results from SeqFeatRs assocpoint.

Usage

volcanoplot(path_to_file_assocpoint_csv_result,
 save_name_pdf, p_values_pos, odds_pos, pos_pos,
 level_of_sig_p, level_of_sig_odds)

Arguments

path_to_file_assocpoint_csv_result

csv file with results from SeqFeatRs assocpoint. For reference see example file.

save_name_pdf

name of file to which results are saved in pdf format.

p_values_pos

column number with p-values.

odds_pos

column number with odds ratios.

pos_pos

column number with positions.

level_of_sig_p

level of significance p values.

level_of_sig_odds

level of significance odds ratios.

Author

Bettina Budeus

Details

Plots log$_10$ Odds ratios versus -log$_10$ p-values and annotates the dots with sequence positions.

Examples

#Input file
if (FALSE) {
assocpoint_result <- system.file("extdata", "assocpoint_results.csv", package="SeqFeatR")

#Usage
volcanoplot(
	path_to_file_assocpoint_csv_result=assocpoint_result,
	save_name_pdf="volcano_plot.pdf",
	p_values_pos = 3,
	odds_pos = 6,
	pos_pos = 1,
	level_of_sig_p = 0.05,
	level_of_sig_odds = 1)
}