clr_transformation: Centered Logratio Transformation
In warrenmcg/sleuth-ALR: Compositional Approach to Sleuth Data Analysis

Description Usage Arguments Details Value

This function applies the centered logratio transformation on a matrix of expression values.

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clr_transformation(mat, base = "e", remove_zeros = FALSE,
  denom_method = "geomean", impute_method = "multiplicative",
  delta = NULL, impute_proportion = 0.65)

`mat`	N x M matrix of estimated abundances
`base`	what should the base of the logarithm be? currently only supports base "e" and base 2.
`remove_zeros`	boolean to see if this function should remove essential zeros (features with zeros in all samples). The default is `FALSE` to be compatible with sleuth, as its default filter removes essential zeros.
`denom_method`	either 'geomean' or 'DESeq2' to use either the geometric mean of all features as the denominator, or the DESeq2-style size factors as the denominator (equivalent to using standard DESeq2-style normalization, which is used in standard sleuth)
`impute_method`	which method to use for imputing zeros. 'multiplicative' (default) sets all values smaller than a imputation value 'delta' (determined by delta or impute_proportion) to that imputation value, and reduces all other values by the amount X * (1 - delta*num_zero_values / sum_constraint). 'additive' is similar to most other tools, and just adds the imputation value to all entries ('delta' must be specified)
`delta`	a number that is the imputed value. If `NULL`, delta = impute_proportion * (minimum value in sample)
`impute_proportion`	percentage of minimum value that becomes the imputed value. Only used if delta is `NULL`

this converts an N x M matrix of N target IDs and M samples (N >> M). If M > N, then the matrix is flipped to do the calculations, but returned with the same as the input. The calculation is as follows: x_1, x_2, ..., x_D => log(x_1 / g(X)), ..., log(x_D / g(X))

N x M matrix of CLR-transformed values with essential zero rows removed.

warrenmcg/sleuth-ALR documentation built on Oct. 27, 2020, 4:30 a.m.