rulesTF0 {TFARM} | R Documentation |
The function substitutes the presence of a given transcription factor
TFi
(or a combination of transcription factors) chosen by the
user with its absence, in the subset of relevant association rules
extracted with the function rulesTF
. Then it searches
for the obtained rules and their quality measures of
support, confidence and lift in the set of most relevant associations
extracted with the function rulesGen
.
A rule is searched in all the association
rules generable from the considered dataset using the function
search_rule
.
rulesTF0(TFi, sub_rules, all_rules, data, RHS)
TFi |
a string, or a string vector: transcription factor (or combination of transcription factors) to remove from the set of rules. |
sub_rules |
a data.frame with a subset of rules containing |
all_rules |
a data.frame with a set of all the rules and their quality measures of support, confidence and lift, to be considered for the search of the obtained rules and their quality measures. |
data |
a GRanges object which contains the Indicator of presence matrix i.e., a matrix with 1 and 0 values representing presence or absence, respectively (in case other values different from 0 are present, all of them are considered as representing presence). |
RHS |
the right-hand-side of the considered association rules. |
A data.frame with all the rules in the set sub_rules
in which the transcription factor (or combination of transcription factors)
TFi
is absent, and their quality measures of support, confidence
and lift.
# Load r_TEAD4 and r_FOSL2 from the data_man collection of datasets: data("data_man") # Load MCF7_chr1: data("MCF7_chr1") r_noFOSL2 <- rulesTF0("FOSL2=1", r_FOSL2, r_TEAD4, MCF7_chr1, "TEAD4=1")