SPRINT

SPRINT is an efficient method to identify genes with spatial expression pattern.
The intended applications are spatially resolved RNA-sequencing from e.g.
Spatial Transcriptomics, or in situ gene expression measurements from
e.g. SeqFISH, Merfish.

System requirements

SPRINT has been tested on R 3.3.1 and is platform independent (tested on Linux, OS X and Windows)
Installation can then be done via the devtools package:

library('devtools')
devtools::install_github('xzhoulab/SPRINT')

Alternatively, installation can then be done from a local binary package from the shell:

R CMD INSTALL SPRINT_1.0.0.tar.gz

Sample Code: Analysis of Breast Cancer Data

    library('SPRINT')
    load("~/data/Layer2_BC_Count.rds")
    ## rawcount matrix of genes by cells/spots
    rawcount[1:5,1:5]

    ## extract the coordinates from the rawdata
    info <- cbind.data.frame(x=as.numeric(sapply(strsplit(colnames(rawcount),split="x"),"[",1)),
                            y=as.numeric(sapply(strsplit(colnames(rawcount),split="x"),"[",2)),
                            total_counts=apply(rawcount,2,sum))
    rownames(info) <- colnames(rawcount)
    ## filter genes and cells/spots and create the SPRINT object for following analysis
    sprint <- CreateSPRINTObject(counts=rawcount, location=info[,1:2],
                                 prectage = 0.1, 
                                 min_total_counts = 10)
    ## total counts for each cell/spot
    sprint@lib_size <- apply(sprint@counts, 2, sum)
    ## Take the first ten genes as an example
    sprint@counts   <- sprint@counts[1:10,]
    ## Estimating Parameter Under Null
    sprint <- sprint.vc(sprint,covariates = NULL, lib_size=sprint@lib_size, num_core=1,verbose=F)
    ## Calculating pval
    sprint <- sprint.test(sprint, check_positive = T, verbose=F)
    ## Check pvals 
    head(sprint@res_mtest[,c("combined_pvalue","adjusted_pvalue")])