Output {NOISeq} | R Documentation

## Output class of NOISeq

### Description

Output object containing the results from differential expression analysis by `noiseq` or `noiseqbio`.

### Slots/List Components

Objects of this class contain (at least) the following list components:

`comparison`: String indicating the two experimental conditions being compared and the sense of the comparison.

`factor`: String indicating the factor chosen to compute the differential expression.

`k`: Value to replace zeroes in orden to avoid inderminations when computing logarithms.

`lc`: Correction factor for length normalization. Counts are divided by length^lc.

`method`: Normalization method chosen. It can be one of "rpkm" (default), "uqua" (Upper Quartile), "tmm" (Trimmed Mean of M) or "n" (no normalization).

`replicates`: Type of replicates: "technical" for technical replicates and "biological" for biological ones.

`results`: R data frame containing the differential expression results, where each row corresponds to a feature. The columns are: Expression values for each condition to be used by `noiseq` or `noiseqbio` (the columns names are the levels of the factor); differential expression statistics (columns "M" and "D" for `noiseq` or "theta" for `noiseqbio`); probability of differential expression ("prob"); "ranking", which is a summary statistic of "M" and "D" values equal to -sign(M)*sqrt(M^2 + D^2), than can be used for instance in gene set enrichment analysis (only when `noiseq` is used); "length" and "GC" of each feature (if provided); chromosome where the feature is ("Chrom"), if provided; start and end position of the feature within the chromosome ("GeneStart", "GeneEnd"), if provided.

`nss`: Number of samples to be simulated for each condition (only when there are not replicates available).

`pnr`: Percentage of the total sequencing depth to be used in each simulated replicate (only when there are not replicates available). If, for instance, pnr = 0.2 , each simulated replicate will have 20% of the total reads of the only available replicate in that condition.

`v`: Variability of the size of each simulated replicate (only used by NOISeq-sim).

### Methods

This class has an specific `show` method in order to work and print a summary of the elements which are contained.

### Author(s)

Sonia Tarazona

[Package NOISeq version 2.28.0 Index]