distStats: Descriptive statistics on intergenic distance data

In pgpmartin/GeneNeighborhood: Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Description

Descriptive statistics on intergenic distance data

Usage

distStats(
  GeneSetDistances,
  confLevel = 0.95,
  nboot = 10000,
  CItype = c("bca", "perc"),
  ncores = NULL
)

Arguments

GeneSetDistances	A tibble with intergenic distances for the different gene sets, as generated by the dist2Neighbors function.
confLevel	Confidence level between 0 and 1.
nboot	Integer (Default to 1e4). Number of bootstrap samples.
CItype	Type of confidence interval ("bca" or "perc").
ncores	Number of cores to use for boostrap.

Value

A tibble with the following columns:

• GeneSet. Name of the gene set.

• Side. Upstream or Downstream.

• Orientation. Orientation of the neighbor (SameStrand or OppositeStrand).

• n. Number of observations.

• Min. Minimum distance.

• Q1. First quartile.

• Median.

• Median_LowerCI. Lower bound of the median bootstrap confidence interval.

• Median_UpperCI. Upper bound of the median bootstrap confidence interval.

• Mean.

• Mean_LowerCI. Lower bound of the mean bootstrap confidence interval.

• Mean_UpperCI. Upper bound of the mean bootstrap confidence interval.

• Q3. Third quartile.

• Max. Maximum distance.

• SD. Standard deviation.

• SEM. Standard Error of the Mean.

NOTE

When nboot is too small and CItype=="bca", the following error can occur: "estimated adjustment 'a' is NA" In this case, use CItype="perc" and/or increase nboot. Using nboot >= 1e4 (the default) is always recommended.

Author(s)

Pascal GP Martin

See Also

boot, boot.ci

Examples

## Obtain gene neighborhood information:
  GeneNeighbors <- getGeneNeighborhood(Genegr)
## Get a (random) set of (100) genes:
  set.seed(123)
  randGenes <- sample(names(Genegr), 100)
## Extract distances for this set of genes and for all genes :
 myGeneSets <- list("RandomGenes" = randGenes,
                    "AllGenes" = GeneNeighbors$GeneName)
 distForGeneSets <- dist2Neighbors(GeneNeighbors,
                                   myGeneSets)
## Obtain descriptive statistics for these sets of genes:
distStats(distForGeneSets,
          nboot = 1e3, CItype = "perc", ncores = 1)

pgpmartin/GeneNeighborhood documentation built on Sept. 2, 2021, 6:37 a.m.