queryCounts: Query dataset for top genes

In LZhang98/nsSNPHotspotViewer: Non-synonymous SNP Distribution Visualization

Description

Filter and sort the given dataset (must be of counts, output by getSNPCounts) based on user- defined parameters.

Usage

queryCounts(countsData, minLength = 0, minCounts = 0, sortBy = "counts")

Arguments

countsData	A dataframe. Output of getSNPCounts.
minLength	The minimum length of genes to filter by. Default is 0 (removes nothing).
minCounts	The minimum number of observed SNPs to filter by. Default is 0 (removes nothing).
sortBy	A string that decides the sorting setting of the output. If none of the below arguments are used, use default sorting. Potentional arguments: counts - The default argument. Sort by decreasing SNP counts. length - Sort by decreasing gene length none - No sorting is performed, and the subset is returned as is.

Value

A subset of the countsData data frame that satisfies the user inputs.

Examples

countsData <- getSNPCounts(snpPositions)
topHits1 <- queryCounts(countsData, 10000, 150)
topHits2 <- queryCounts(countsData, 10000, 150, sortBy="length")
topHits3 <- queryCounts(countsData, 10000, 150, sortBy="asdf")

LZhang98/nsSNPHotspotViewer documentation built on Dec. 31, 2020, 2:14 p.m.