Linnorm.SGenes: Linnorm model stable gene selection tool.

In Linnorm: Linear model and normality based normalization and transformation method (Linnorm)

Description

For datasets without spike-ins and for users who do not wish to rely on spike-ins, we provide this model stable gene selection tool.

Usage

Linnorm.SGenes(datamatrix, RowSamples = FALSE, showinfo = FALSE,
  minNonZeroPortion = 0.75, F_p = 0.3173, F_LC_Genes = "Auto",
  F_HC_Genes = 0.01, max_F_LC = 0.75)

Arguments

datamatrix	The matrix or data frame that contains your dataset. Each row is a feature (or Gene) and each column is a sample (or replicate). Raw Counts, CPM, RPKM, FPKM or TPM are supported. Undefined values such as NA are not supported. It is not compatible with log transformed datasets.
RowSamples	Logical. In the datamatrix, if each row is a sample and each row is a feature, set this to TRUE so that you don't need to transpose it. Linnorm works slightly faster with this argument set to TRUE, but it should be negligable for smaller datasets. Defaults to FALSE.
showinfo	Logical. Show algorithm running information. Defaults to FALSE.
minNonZeroPortion	Double >=0, <= 1. Minimum non-Zero Portion Threshold. Genes not satisfying this threshold will be removed. For exmaple, if set to 0.75, genes without at least 75 percent of the samples being non-zero will be removed. Defaults to 0.75.
F_p	Double >=0, <= 1. Filter genes with standard deviation and skewness less than this p value. Defaults to 0.3173.
F_LC_Genes	Double >= 0.01, <= 0.95 or Character "Auto". Filter this portion of the lowest expressing genes. It can be determined automatically by setting to "Auto". Defaults to "Auto".
F_HC_Genes	Double >=0, <= 1. Filter this portion of the highest expressing genes. Defaults to 0.01.
max_F_LC	Double >=0, <= 0.95. When F_LC is set to auto, this is the maximum threshold that Linnorm would assign. Defaults to 0.75.

Details

This function selects stable genes from the dataset using the Linnorm's algorithm.

Value

This function returns a data matrix that contains stable genes only.

Examples

#Obtain example matrix:
data(Islam2011)
#Transformation:
StableGenes <- Linnorm.SGenes(Islam2011)

Linnorm documentation built on Nov. 8, 2020, 6:48 p.m.