volcanoplot: Create volcano plot
In SeqFeatR: A Tool to Associate FASTA Sequences and Features

Description Usage Arguments Details Author(s) Examples

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

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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)

`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.

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

Bettina Budeus

#Input file
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)