Calculates the estimate and confidence interval of a module-level statistic based on all values obtained by jackknifing the module.
Usage
summarizeJackknifeStats(
stats_df,
stats = setdiff(colnames(stats_df), c("regulator", "type", "id", "gene_removed",
"module_size", "replicate", "species", "replicate1", "replicate2", "species1",
"species2")),
summary_method = ifelse(endsWith(stats, "monophyl"), "mean", "median"),
conf_level = 0.95
)Arguments
- stats_df
Data frame of the statistics per jackknife module version:
- regulator
Character, transcriptional regulator.
- module_size
Integer, the numer of target genes assigned to a regulato.r
- type
Character, module type (orig = original or jk = jackknifed).
- id
Character, the unique ID of the module version (format: nameOfRegulator_jk_nameOfGeneRemoved in case of module type 'jk' and nameOfRegulator_orig in case of module type 'orig').
- gene_removed
Character, the name of the gene removed by jackknifing (NA in case of module type 'orig').
- replicate
Character, the name of the replicate (optional, only needed if the statistics are calculated per replicate).
- species
Character, the name of the species (optional, only needed if the statistics are calculated per replicate or per species).
- replicate1, replicate2
Character, the names of the replicates compared (optional, only needed if the statistics are calculated per replicate pair).
- species1, species2
Character, the names of the species compared (optional, only needed if the statistics are calculated per replicate pair or species pair).
- {{nameOfStat}}
Numeric, integer or logical, one or more columns containing the values of the statistic(s) specified in 'stats'.
- stats
Character, the name of the statistic(s) that need to be summarized.
- summary_method
Character or character vector, the summary method ("mean" or "median") to be used for the statistics in 'stats'. If only one value is provided, the same summary method will be used for all statistics, if a vector is provided, each element of the vector will be used for the corresponding element in 'stats'. By default, "mean" for statistics measuring monophyleticity and "median" for all other statistics.
- conf_level
Numeric, confidence level of the interval (default: 0.95).
Value
A data frame of the statistics per module:
- regulator
Character, transcriptional regulator.
- module_size
Module size, the numer of target genes assigned to a regulator.
- replicate
The name of the replicate (only if the column is present in the input 'stats_df').
- species
The name of the species (only if the column is present in the input 'stats_df').
- replicate1, replicate2
The names of the replicates compared (only if the column is present in the input 'stats_df').
- species1, species2
The names of the species compared (only if the column is present in the input 'stats_df').
- {{nameOfStat}}
Numeric, one or more columns containing the estimates (mean or median) of the statistic(s) specified in 'stats'.
- var_{{nameOfStat}}
Numeric, one or more columns containing the variances of the statistic(s) specified in 'stats'.
- lwr_{{nameOfStat}}
Numeric, one or more columns containing the lower bounds of the confidence interval for the statistic(s) specified in 'stats'.
- upr_{{nameOfStat}}
Numeric, one or more columns containing the upper bounds of the confidence interval for the statistic(s) specified in 'stats'.
Details
To gain information about the confidence of various statistics, jackknifing can be used: each member gene of a module is removed and the statistics are re-calculated. This way, the median or mean and its confidence interval across the jackknifed versions can be used to estimate a statistic of interest for the module as a whole. For continuous statistics the median, for boolean statistics the mean is recommended as the summary method.
Examples
pres_stats <- summarizeJackknifeStats(pres_stats_jk)
tree_stats <- summarizeJackknifeStats(tree_stats_jk,
c("total_tree_length", "within_species_diversity"))