Create a SRTProject object

Create a SRTProject object based on at least count matrix list and spatial coordinates list.

CreateSRTProject(
  cntList,
  coordList,
  projectName = "SRTProject",
  cellMetaDataList = NULL,
  sampleMetadata = NULL,
  min.spots = 0,
  min.genes = 0,
  filter.plot = FALSE,
  prefix = "****",
  force = FALSE,
  verbose = TRUE
)

Arguments

cntList

a list with each component as a count matrix, has names for all components.

coordList

a list with spatial coordinates matrix has the same names as that of cntList.

projectName

a string, the name of this project, default as "SRTProject".

cellMetaDataList

a list or NULL, provide the cell meta data for each data batch.

sampleMetadata

a dataframe object with the number of rows same as the length of cntList, provide the sample meta data.

min.spots

a non-negative integer, the least number of nonzero spots for a retained gene used to filter spots in the QC.

min.genes

a non-negative integer, the least number of nonzero genes for a retained spot used to filter spots in the QC.

filter.plot

a logical value, whether plot the QC plots in filtering step.

prefix

a string, specify the prefix for the output information.

force

a logical value, whether delete then rewrite the data to h5 file if the project exists.

verbose

a logical value, whether output the information when creating a SRTProject object.