TFilter: TFilter:
In nathansam/CircadianTools: Collection of Tools for Detecting Rhythmic Genes

Description Usage Arguments Value Examples

Applies a filter where a t-test is carried out on gene activity levels between time points. The number of significant changes between time points is found. If there is a sufficient number of significant changes and close to as many positive changes as negative changes then the gene is included in the filtered dataset.

TFilter(
  dataset,
  maxdifference = 1,
  minchanges = 2,
  psignificance = 0.05,
  nthreads = NULL
)

`dataset`	A transcriptomics dataset. First columns should be gene names. All other columns should be expression levels.
`maxdifference`	The maximum difference between the number of signifcant positive t statistic and the number of signifcant negative t statistic.
`minchanges`	The minimum number of significant changes found via t-tests for the gene to be included in the filtered dataset.
`psignificance`	The maximum p-value for which a result of a t-test is classed as significant.
`nthreads`	Number of processor threads to be used for calculating the distance matrix. If not specified then the maximum number of logical cores are used.