ExtractDB: ExtractDB

In rubystokes/ECPT_Package:

Usage

ExtractDB(x)

Arguments

x

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (x)
{
    tbl(SLAS2, "Per_Cell") %>% left_join(tbl(SLAS2, "Per_Image")) %>%
        select(Img_N = ImageNumber, Experiment = Image_Metadata_Experiment,
            Img_Nuclei_N = Image_Count_Nuclei, Cell_Type = Image_Metadata_Cell,
            Treatment = Image_Metadata_Treatment, Replicate = Image_Metadata_Replicate,
            Well = Image_Metadata_Well, Cell_N = Cell_Number_Object_Number,
            Cell_VEC_MeanI = Cell_Intensity_MeanIntensity_VECOrig) %>%
        collect() %>% cbind(tbl(SLAS2, "Cell_ActCl") %>% select(Cell_Act_Cl = class) %>%
        collect()) %>% cbind(tbl(SLAS2, "Per_CellJunctArea") %>%
        select(Junct_VEC_MeanI = CellJunctArea_Intensity_MeanIntensity_VECOrig) %>%
        collect()) %>% cbind(tbl(SLAS2, "Per_CellsObj") %>% select(Cell_NCheck = CellsObj_Number_Object_Number,
        Cell_Area = CellsObj_AreaShape_Area, Cell_Perim = CellsObj_AreaShape_Perimeter,
        Cell_MaxL = CellsObj_AreaShape_MajorAxisLength, Cell_MinL = CellsObj_AreaShape_MinorAxisLength,
        Cell_Orientation = CellsObj_AreaShape_Orientation, Cell_Neighbour_N = CellsObj_Neighbors_NumberOfNeighbors_Expanded,
        Cell_1st_Nb_Dist = CellsObj_Neighbors_FirstClosestDistance_Expanded,
        Cell_2nd_Nb_Dist = CellsObj_Neighbors_SecondClosestDistance_Expanded,
        Perc_Touch = ) %>% collect()) %>% cbind(tbl(SLAS2, "Per_Nuclei") %>%
        select(Nu_X = Nuclei_Location_Center_X, Nu_Y = Nuclei_Location_Center_Y,
            DNA_IntI = Nuclei_Intensity_IntegratedIntensity_Nuclei,
            Nu_Clustering = Nuclei_Neighbors_NumberOfNeighbors_20,
            Nu_1st_Nb_Dist = Nuclei_Neighbors_FirstClosestDistance_20,
            Nu_2nd_Nb_Dist = Nuclei_Neighbors_SecondClosestDistance_20,
            Nu_Area = Nuclei_AreaShape_Area) %>% collect()) %>%
        cbind(tbl(SLAS2, "Per_NDotsCy") %>% select(Cy_NCH_IntI = NDotsCy_Intensity_IntegratedIntensity_NOTCH) %>%
            collect()) %>% cbind(tbl(SLAS2, "Per_NDotsNu") %>%
        select(Nu_NCH_IntI = NDotsNu_Intensity_IntegratedIntensity_NOTCH) %>%
        collect()) %>% cbind(tbl(SLAS2, "Per_CellsObj") %>% select(Stb_J_N = CellsObj_Children_Stb_Count,
        Lin_J_N = CellsObj_Children_Lin_Count, Jag_J_N = CellsObj_Children_Jag_Count,
        NaJ_J_N = CellsObj_Children_NaJ_Count) %>% collect())
  }

rubystokes/ECPT_Package documentation built on Dec. 22, 2021, 8:12 p.m.