FIT: Run FIT pipeline

In shenorrLab/FIT.mouse2man: Predicts human disease relevant genes from mouse model gene expression, based on prior mouse and human gene expression comparisons

Description

This function runs the whole FIT pipeline: checks input file format, pre-processes data (for microarray data only) and computes predictions.

Usage

FIT(MouseFile, DataType)

Arguments

MouseFile	File name that includes the mouse data, in CSV format
DataType	Either "microarray" or "rnaseq", depending on the technology by which the data was assayed.

Value

A data.frame containing the following columns:

• Mouse.Entrez, Human.Entrez, Mouse.symbol, Human.symbol - Gene IDs

• Mouse_FoldChange - Mouse fold-change as computed from the mouse input data

• Mouse_Ztest - Mouse Z-test values as computed from the mouse input data

• FIT_prediction - Human effect-size prediction by the FIT model

• FIT_percentile - Percentiles of absolute values of FIT's predictions

• UpDown - Sign of prediction

• CI_low, CI_low, CI_size, CI_percentile - Confidenc einterval values (low, high), overall size (high-low) and percentile

shenorrLab/FIT.mouse2man documentation built on May 30, 2019, 11:44 a.m.