amanida (version 0.3.0)

amanida_report: Report

Description

amanida_report creates a report from the data using amanida functions

Usage

amanida_report(
  input_file,
  separator = NULL,
  analysis_type = NULL,
  column_id,
  pvalue_cutoff = NULL,
  fc_cutoff = NULL,
  votecount_lim,
  path = NULL,
  comp_inf = NULL
)

Value

an html document saved in the working directory

Arguments

input_file

path to the original dataset in xlsx, xls, csv or txt format

separator

indicate the separator used in the input_file parameter

analysis_type

indicate if data will be quantitative, qualitative or both. Options are:

• "quan-qual" for quantitative and qualitative meta-analysis

• "quan" for quantitative meta-analysis using p-value and fold-change

• "qual" for qualitative meta-analysis using trend label

column_id

vector containing columns names to use. It has to be in order identification, p-values, fold-changes, sample size and reference.

pvalue_cutoff

numeric value to consider statistical significance

fc_cutoff

numeric value to consider significance for effect size

votecount_lim

minimum numeric value for vote-counting visualization

path

path to the directory where html file is created, otherwise the file will be saved in a temporal folder

comp_inf

name checking using information from public databases

Details

This function uses directly the dataset to create a report with the meta-analysis results. In case of quantitative analysis amanida_report uses the functions amanida_read and compute_amanida for analyse the input data. Then the results are showed using volcano_plot, explore_plot and vote_plot.

Examples

if (FALSE) {
column_id = c("Compound Name", "P-value", "Fold-change", "N total", "References")
input_file <- getsampleDB()

amanida_report(input_file, separator = ";", column_id, analysis_type = "quan", 
                pvalue_cutoff = 0.05, fc_cutoff = 4, votecount_lim = 2, 
                comp_inf = F)
}