toprnk: toprnk

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

toprnk

Description

This function execute toprnk analysis which search for correspondence between clusters of two different experiments using clusters-pseudobulks, zscored on rows, and the cluster specific genes from comet analysis. Thus, the function clustersBulk and cometsc have to be run in the two datasets before their comparison.

Usage

toprnk(
  group = c("sudo", "docker"),
  scratch.folder,
  fileX,
  fileY,
  separatorX,
  separatorY,
  xCometFolder,
  yCometFolder,
  top.ranked = 320,
  outputFolder
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the path of the scratch folder
fileX	a character string indicating the path of the pseudobulkRow file, with file name and extension included.
fileY	a character string indicating the path of the pseudobulkRow file, with file name and extension included.
separatorX	separator used in count file, e.g. '\t', ','
separatorY	separator used in count file, e.g. '\t', ','
xCometFolder	path of Comet results from X experiment
yCometFolder	path of Comet results from Y experiment
top.ranked	MAX number of top comet genes to be used for each cluster, default 320
outputFolder	where results are placed

Value

A folder called XYpb with all the results generated. The function produces an integrated output combining 7 thresholds from top.ranked (top.ranked, top.ranked/2, top.ranked/4, top.ranked/8, top.ranked/16/ top.ranked/32, top.ranked/64) over Pearsons in steps of 01 from 1 to 0.5. XYpb_topZZ.csv can be used to generate HCL. XYpb_cor_0.K_toprnk_ZZ.csv contain the associated clusters given a Pearson correlation threshold of 0.K. The files XYpb_cor_0.K_toprnk_ZZ_CSS_0.H.csv, are the subset of clusters that have a specific cell stability score, we suggest to associate only clusters with at least 0.5 CSS. If validation is TRUE it will be estimated for the chosen XYpb_cor_0.K_toprnk_ZZ.csv a p-value, which is calculated performing correlation between clusters, using randomly selected ZZ genes * cls, and repeating this procedure 1000 times.

Author(s)

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
 library(rCASC)
 toprnk(group="docker", 
        scratch.folder="/scratch", 
        fileX="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_NT_2_clx/VandE/VandE_bulkRow.csv",
        fileY="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_cetux_2_clx/VandE/VandE_bulkRow.csv", 
        separatorX=",",
        separatorY=",",
        xCometFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_NT_2_clx/VandE/Results/VandE/8/outputdata",
        yCometFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_cetux_2_clx/VandE/Results/VandE/8/outputdata",
        top.ranked=320,
        outputFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX"
 )

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.