fluorescence.selection: Ranking genes from fluorescence selection data

In wolfsonliu/FluorescenceSelection: Bird migration staging modeling

Description

Function for calculation of gene ranks from fluorescence enriched screening data.

Usage

fluorescence.selection(
  gene,
  sgrna,
  barcode,
  reference,
  fluorescence,
  selection.ratio,
  n.to.consider = NA
)

Arguments

gene	vector of character, gene names.
sgrna	vector of character, sgrna sequences or names.
barcode	vector of character, barcode sequences or names.
reference	vector of integer, raw counts of barcodes in reference group.
fluorescence	vector of integer, raw counts of barcodes in fluorescence group.
selection.ratio	numeric, value should be in (0, 1), the ratio of cells in fluorescence group which were selected from reference group.
n.to.consider	integer, the number of barcodes to be used for ranking of genes. Genes with more barcodes than n.to.consider will be ranked by randomly sampled barcodes (with bootstrapping to make stable results).

Value

returns the fs data type, which is a list containing gene ranks, barcode data, and analysis parameters.

Examples

result <- fluorescence.selection(
    gene, sgrna, barcode, reference, fluorescence, selection.ratio=0.01
)

wolfsonliu/FluorescenceSelection documentation built on Sept. 14, 2020, 9:01 p.m.