Man pages for CONDOP
Condition-Dependent Operon Predictions

comp.gene.transc.levelsCompile the transcription levels for the coding regions.
comp.igr.transc.levelsCompile the transcription levels for the intergenic regions.
compile.confirmed.operonsCompile a set of coinfirmed operons.
CONDOP-packageDevelop ensemble classifiers for condition-dependent operon...
ct1Coverage Vector 1
detect.sid.pointsFind strat/end transcription points.
getCondOperonMapBuild the condition-dependent operon map for a given RNA-seq...
get.infoGet generic info about the door operons that have been...
get.intergenic.regionsBuild a data table containing generic information on...
get.NCBI.seqFind and get a genome sequence by specifyng the accession...
get.operon.end.pointsDetermine operon end-points (OEPs).
get.operon.start.pointsDetermine operon start-points (OSPs).
join.genes.and.operonsJoin gene(s) and operon(s) annotations.
pred.operon.statusPredict operon status of gene pairs (e.g., POPs, DOPs,...).
pre.procPrepare data inputs for the main function 'run.CONDOP()'.
pre.processingNormalize the data before the classification step.
qcutDetermine cutoff values for a given RNA-seq expression...
read.annot.from.gffRead a GFF file from NCBI and return a GRanges object.
read.door.annotationsRead the operon(s) data file downloaded from...
read.gff.annotationsRead gene annotations in GFF format
remove.cov.depth.from.aFeatRemove the read coverage on a given feature (e.g. rRNA and...
run.CONDOPBuild condition-dependent operon maps.
select.nopsDefine a set of NOPs which is used to train the operon...
select.opsDefine a set of OPs which is used to train the operon...
select.ops.indoorDefine the set of OPs annotated in DOOR.
select.popsDefine a set of gene pairs POPs with an "operon status" to...
sum.conf.matrixProvide classification metrics.
test.corrStatistical test to find a putative transcription start (or...
train.RFsTrain and validate the operon classifier and evaluate the...
tune.clsTune and build the classification models.
validate.clsValidate the classification models.
CONDOP documentation built on May 30, 2017, 4:31 a.m.