ks.miRNA_differential_expression: ks.miRNA_differential_expression

In kstawiski/miRNAselector: miRNAselector - a package for biomarker selection based on high-throughput experiments.

Description

The variable performes standard differential expression analysis using unpaired t-test with BH and Bonferonni correction. It requires 'ttpm_pofiltrze' object, which is a matrix of log-transformed TPM-normalized miRNAs counts with miRNAs placed in 'ttpm' design (i.e. columns and cases placed as rows). Classess should be passed as 'klasy' and this should be a vector of length equal to number of rows in 'ttpm_polfiltrze' and contain only "Cancer" or "Control" labels!! The function returns the miRNAs sorted by BH-corrected p-value.

Usage

ks.miRNA_differential_expression(ttpm_pofiltrze, klasy, mode = "auto")

Arguments

ttpm_pofiltrze	matrix of log-transformed TPM-normalized miRNAs counts with miRNAs placed in 'ttpm' design (i.e. columns and cases placed as rows)
klasy	vector describing label for each case. It should contain only "Cancer" and "Control" labeles!!!!
mode	use 'logtpm' for log(TPM) data or 'deltact' for qPCR deltaCt values. This parameters sets how the fold-change is calculated. Setting it to "auto" will try to read settings from var_type.txt (used in docker).

Value

Data frame with results.

kstawiski/miRNAselector documentation built on Oct. 10, 2020, 9:03 a.m.