getFeaturesAllSpots
(Package: PGPC) :
Function used to segment all spots for a well
getFeaturesAllSpots is called by the function extractFeatures to segment the images of the screen
● Data Source:
BioConductor
● Keywords:
● Alias: getFeaturesAllSpots
●
0 images
|
getInteractions
(Package: PGPC) :
Function to calculate chemical genetic interactions
To detect chemcial genetic interactions, the data of each feature is modeled using a multiplicative model and robust L1 regression to estimate the effects of the cell line and drug treatment using the medpolish function. In this iterative approach row and column median values are subtracted alternately until the proportional change of the absolute residuals falls below a defined threshold. The final row and column values describe the drug and cell line effect respectively. The residuals represent the interaction terms. This process is done for each replicate and each feature individually. To detect significant interactions the values of replicates are used to perform a moderated t-test against the null hypothesis t = 0, using the implementation in the Bioconductor package limma. p-values are adjusted for multiple testing by controlling for the false discovery rate using the method of Benjamini & Hochberg.
● Data Source:
BioConductor
● Keywords:
● Alias: getInteractions
●
0 images
|
mergeProfiles
(Package: PGPC) :
Function to merge profiles of extracted features from parallel
Merges all feature profiles of each well and saves the result in the specified file.
● Data Source:
BioConductor
● Keywords:
● Alias: mergeProfiles
●
0 images
|
segmentAllSpots
(Package: PGPC) :
Function used to segment all spots for a well
segmentAllSpots is called by the imageHTS function segmentWells to segment the images of the screen
● Data Source:
BioConductor
● Keywords:
● Alias: segmentAllSpots
●
0 images
|
segmentXman
(Package: PGPC) :
Function used to segment a single image
segmentXman is called by the function segmentAllSpots to segment the single image of one spot.
● Data Source:
BioConductor
● Keywords:
● Alias: segmentXman
●
0 images
|
summarizeWellsExtended
(Package: PGPC) :
Function to summarize the extracted features per cell for each well
The function extends the imageHTS function summarizeWells. It calculates summary statistics over all cells for each well. In particular the trimmed mean (trim = 0.1) and sd is calculated for each extracted feature. Additionally the 1 calculated for features that are not the standard deviation, median absolut deviation or Halralick statistics calculated over each cell.
● Data Source:
BioConductor
● Keywords:
● Alias: summarizeWellsExtended
●
0 images
|
providing 
.