Output class of NOISeq
Output object containing the results from differential expression analysis by
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
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.