cellHTS2-package |
cellHTS2 Package Overview |
annotate |
Annotates the reagents (probes) of a cellHTS object |
annotate,cellHTS-method |
Annotates the reagents (probes) of a cellHTS object |
batch |
Access and replace the batch information of a cellHTS object |
batch,cellHTS-method |
Access and replace the batch information of a cellHTS object |
batch<- |
Access and replace the batch information of a cellHTS object |
batch<-,cellHTS,data.frame-method |
Access and replace the batch information of a cellHTS object |
bdgpbiomart |
Dataset with annotation of CG identifiers |
Bscore |
B score normalization |
cellHTS |
A class for data from cell-based high-throughput assays
performed in plate format. |
cellHTS-class |
A class for data from cell-based high-throughput assays
performed in plate format. |
cellHTS2 |
cellHTS2 Package Overview |
class.cellHTS |
A class for data from cell-based high-throughput assays
performed in plate format. |
coerce,chtsImage,data.frame-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
compare2cellHTS |
A class for data from cell-based high-throughput assays
performed in plate format. |
compare2cellHTS,cellHTS,cellHTS-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
configurationAsScreenPlot |
Screen plot of the plate configuration of a cellHTS object |
configure |
Configures the plates and plate result files |
configure,cellHTS-method |
Configures the plates and plate result files |
convertOldCellHTS |
Convert an old S3 class cellHTS object to the new S4 class cellHTS object |
convertWellCoordinates |
Converts different well identifiers |
Data |
Access and replace the assayData slot of a cellHTS object |
Data,cellHTS-method |
Access and replace the assayData slot of a cellHTS object |
Data<- |
Access and replace the assayData slot of a cellHTS object |
Data<-,cellHTS,array-method |
Access and replace the assayData slot of a cellHTS object |
dualCh |
A sample cellHTS object containing dual channel data |
geneAnno |
Access the annotation from a cellHTS object. |
geneAnno,cellHTS-method |
Access the annotation from a cellHTS object. |
getDynamicRange |
Per-plate dynamic range of a cellHTS object |
getEnVisionCrosstalkCorrectedData |
Read a plate file obtain from EnVision Plate Reader |
getEnVisionRawData |
Read a plate file obtain from EnVision Plate Reader |
getMeasureRepAgreement |
Measures of agreement between plate replicates from a cellHTS object |
getSettings |
cellHTS2 HTML report settings |
getTopTable |
Generate the hit list from a scored cellHTS object |
getZfactor |
Per-experiment Z'-factor of a cellHTS object |
gseaModule |
Constructor for an object of class gseaModule |
imageScreen |
Experiment-wide quality control plot of a cellHTS object |
initialize,cellHTS-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
intensityFiles |
Retrieve the contents of the input files used to generate a given cellHTS object. |
intensityFiles,cellHTS-method |
Retrieve the contents of the input files used to generate a given cellHTS object. |
KcViab |
A sample cellHTS object - D. melanogaster genome-wide RNAi screen |
KcViabSmall |
A sample cellHTS object - D. melanogaster genome-wide RNAi screen |
length,GeneSet-method |
Constructor for an object of class gseaModule |
lines,ROC-method |
Creates an object of class "ROC" which can be plotted as a ROC curve |
meanSdPlot |
A class for data from cell-based high-throughput assays
performed in plate format. |
meanSdPlot,cellHTS-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
name |
A class for data from cell-based high-throughput assays
performed in plate format. |
name,cellHTS-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
name<- |
A class for data from cell-based high-throughput assays
performed in plate format. |
name<-,cellHTS,character-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
nbatch |
A class for data from cell-based high-throughput assays
performed in plate format. |
nbatch,cellHTS-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
normalizePlates |
Per-plate data transformation, normalization and variance adjustment |
oldKcViabSmall |
A sample S3 class cellHTS object - D. melanogaster genome-wide RNAi screen |
oneRowPerId |
Rearrange dataframe entries such that there is exactly one row
per ID. |
pdim |
Retrieve information related with the format of a RNAi experiment |
pdim,cellHTS-method |
Retrieve information related with the format of a RNAi experiment |
plate |
Retrieve information related with the format of a RNAi experiment |
plate effects |
Per-plate data transformation, normalization and variance adjustment |
plate,cellHTS-method |
Retrieve information related with the format of a RNAi experiment |
plateConf |
Retrieve the contents of the input files used to generate a given cellHTS object. |
plateConf,cellHTS-method |
Retrieve the contents of the input files used to generate a given cellHTS object. |
plateEffects |
Access plate effects stored in a cellHTS object. |
plateEffects,cellHTS-method |
Access plate effects stored in a cellHTS object. |
plateList |
Retrieve the contents of the input files used to generate a given cellHTS object. |
plateList,cellHTS-method |
Retrieve the contents of the input files used to generate a given cellHTS object. |
plot,ROC,missing-method |
Creates an object of class "ROC" which can be plotted as a ROC curve |
plotSpatialEffects |
Plate plot with the row and column offsets estimated by the a spatial normalization method |
position |
Retrieve information related with the format of a RNAi experiment |
position,cellHTS-method |
Retrieve information related with the format of a RNAi experiment |
readHTAnalystData |
Read a set of plate results obtained from a HTanalyser plate reader |
readPlateList |
Read a collection of plate reader data files |
ROC |
Creates an object of class "ROC" which can be plotted as a ROC curve |
ROC,cellHTS-method |
Creates an object of class "ROC" which can be plotted as a ROC curve |
ROC-class |
Class that contain data that can be plotted as a ROC curve. |
scoreReplicates |
Scores normalized replicate values given in a cellHTS object |
scores2calls |
Sigmoidal transformation of the score values stored in a cellHTS object obtaining the call values for each probe. |
screenDesc |
Retrieve the contents of the input files used to generate a given cellHTS object. |
screenDesc,cellHTS-method |
Retrieve the contents of the input files used to generate a given cellHTS object. |
screenLog |
Retrieve the contents of the input files used to generate a given cellHTS object. |
screenLog,cellHTS-method |
Retrieve the contents of the input files used to generate a given cellHTS object. |
setSettings |
cellHTS2 HTML report settings |
settings |
cellHTS2 HTML report settings |
show,cellHTS-method |
A class for data from cell-based high-throughput assays
performed in plate format. |
show,ROC-method |
Class that contain data that can be plotted as a ROC curve. |
spatialNormalization |
Spatial normalization |
state |
Retrieve the state of a cellHTS object. |
state,cellHTS-method |
Retrieve the state of a cellHTS object. |
summarizeChannels |
Summarization of dual-channel data |
summarizeReplicates |
Summarize between scored replicate values given in a cellHTS object to obtain a single value for each probe |
templateDescriptionFile |
Creates a template description file for an RNAi experiment |
updateCellHTS |
Update old serialized cellHTS objects. |
well |
Retrieve information related with the format of a RNAi experiment |
well,cellHTS-method |
Retrieve information related with the format of a RNAi experiment |
wellAnno |
Access the annotation from a cellHTS object. |
wellAnno,cellHTS-method |
Access the annotation from a cellHTS object. |
write.tabdel |
Wrapper to function 'write.table' used to write data to a
tab-delimited file |
writeReport |
Create a directory with HTML pages of linked tables and plots
documenting the contents of a cellHTS experiment |
writeTab |
Write the data from a cellHTS object to a tab-delimited file |
writeTab,cellHTS-method |
Write the data from a cellHTS object to a tab-delimited file |