Description Slots/List Components Methods Author(s)

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

or `noiseqbio`

.

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).

This class has an specific `show`

method in order to work and print a summary of the elements which are contained.

Sonia Tarazona

NOISeq documentation built on May 31, 2017, 2:42 p.m.

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