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fcros (version 1.6.1)

A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

Description

A fold change rank based method is presented to search for genes with changing expression and to detect recurrent chromosomal copy number aberrations. This method may be useful for high-throughput biological data (micro-array, sequencing, ...). Probabilities are associated with genes or probes in the data set and there is no problem of multiple tests when using this method. For array-based comparative genomic hybridization data, segmentation results are obtained by merging the significant probes detected.

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Version

Install

install.packages('fcros')

Monthly Downloads

281

Version

1.6.1

License

GPL (>= 2)

Maintainer

Doulaye Dembele

Last Published

May 31st, 2019

Functions in fcros (1.6.1)

Plot a chromosome data

Calculation of the sorted rank matrix from the dataset

Plot a chromosome segmentation results

Segmentation of a chromosome data

Example of aCGH "info file" for the fcros package.

Calculation of the sorted rank matrix from the dataset

Summarization of the detection results for a list of chromosomes

Example of aCGH "data file" for the fcros package.

Example of sequencing data to test the rankReads function.

Using a C code for merging chromosome segments

Calculation of fold change using pairwise comparison values

Search for the top N changed genes or probes

Search for the top N changed genes or probes using f-values

Example of dataset for the fcros package.

Read a tab delimited text file

Transformation of read count values

This function computes a score to assess the significance of sequencing values

Writing the fcros() or pfco() results in a tab delimited text file

Searching for differentially expressed genes/probes using an approach based on the Perron-Frobenius theorem

Calculation of the mean and the standard deviation of the full or reduced matrix of sorted ranks

Student t-test for detecting differentially expressed genes

pvalVolcanoPlot

Performs a volcano plot of the FCROS/PFCO statistics

Search for differentially expressed genes/probes

Search for differentially expressed genes/probes

Calculation of the Student one sample test probabilities

Calculation of a matrix of fold changes using pairwise comparisons

Compute variance of a beta distribution from data

A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

fvalVolcanoPlot

Performs a volcano plot of the FCROS/PFCO statistics

Search for differentially expressed genes or to detect recurrent copy number aberration probes

Search for the top N changed genes or probes using p-values

Determine numerically a threshold for the ranking score

Histogram plot function of the fcros package results

Calculation of the FC matrix using pairwise comparisons

Calculation of the reduced matrix containing sorted rank values

Performs a total count normalization of reads

Searching for differentially expressed genes or detecting recurrent copy number aberration probes using an approach based on the Perron-Frobenius theorem