Generate a Table with Fold Change even if the factor has more than 2 levels
gentab_FC_more_than2levels.RdGiven a dataframe and a set of numerical variables of that dataframe, it performs fold changes analysis for each pair of levels of a desired variable and creates a new table.
Usage
gentab_FC_more_than2levels(
df,
v,
f,
second_to_first_ratio = TRUE,
paired = FALSE,
are_log_transf = FALSE,
log_base = 2,
only_on_positive = FALSE
)Arguments
- df
a dataframe.
- v
a character vector. Each element must correspond to a column name of the df, each of which must contain numeric values.
- f
character vector of length 1. Name of the column of df containing the factor variable considered for performing the Fold Change analysis.
- second_to_first_ratio
logical. If TRUE the second group/first group ratio will be computed, if FALSE the first group/second group ratio will be computed.
- paired
logical. If FALSE it performs FC on mean of the two groups. If TRUE it performs FC for each pair and then compute the mean.
- are_log_transf
logical. If you really need to perform this FC analysis on already log-transformed data, specify here as TRUE, and the subtraction will be performed instead of the ration.
- log_base
numeric of length 1. Specify here the base of the logarithm to calculate the logFC or, if are_log_transf is TRUE; the base of the logarithm the that were used to transform the data.
- only_on_positive
logical. If TRUE, FC analysis will be performed only if all values are positive (if paired), or if all means are positive (if not paired). The rest will be left as NA.