View source: R/amanida_report.R
amanida_report | R Documentation |
amanida_report
creates a report from the data using amanida functions
amanida_report( input_file, separator = NULL, analysis_type = NULL, column_id, pvalue_cutoff = NULL, fc_cutoff = NULL, votecount_lim, path = NULL, comp_inf = NULL )
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:
|
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 |
complete information of compounds from public databases |
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
.
an html document saved in the working directory
## Not run: 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) ## End(Not run)
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