prepare_tables: prepare_tables This data prepares CellProfiller style input...

In BodenmillerGroup/neighbouRhood: neighbouRhood analysis in R

Description

prepare_tables This data prepares CellProfiller style input tables into standardized tables optimized for the neightbourhood analysis.

Usage

prepare_tables(
  dat_obj,
  dat_rel,
  objname = DEFAULTOBJNAME,
  relationship = DEFAULTRELATIONSHIP,
  col_imnr = IMGNR,
  col_objnr = OBJNR,
  col_label = LABEL,
  col_group = NULL,
  col_relationship = RELATIONSHIP,
  col_objname = OBJNAME
)

Arguments

dat_obj	an object level data.table from cellprofiler
dat_rel	a relationship table from cellprofiler
objname	the objectname of the object table
relationship	the relationship table
col_imnr	the image number column
col_objnr	the object number column
col_label	the label/cluster number to do the permutation test on
col_group	a grouping to do the permutation test with, default: do it per image
col_relationship	the column name for the relationship column
col_objname	the column for the object name column

Value

returns the percentile of each value of x a list with elements:

[[1]] a obj table with columns: 'ObjectID': a new, integer ID from 1:N 'label': the group/cluster label of the cells 'ImageNumber': the CP imagenumber 'ObjectNumber': the CP objectnumber 'Group': The group to do the permutations by 'ObjectName': The object name

[[2]] a relationship table with columns: 'First Object ID': Id of the first object 'Second Object ID': Id of the second object 'Group': the group to which the relationship belongs

BodenmillerGroup/neighbouRhood documentation built on Sept. 9, 2021, 4:49 a.m.