pagoda.subtract.aspect {scde} | R Documentation

## Control for a particular aspect of expression heterogeneity in a given population

### Description

Similar to subtracting n-th principal component, the current procedure determines (weighted) projection of the expression matrix onto a specified aspect (some pattern across cells, for instance sequencing depth, or PC corresponding to an undesired process such as ribosomal pathway variation) and subtracts it from the data so that it is controlled for in the subsequent weighted PCA analysis.

### Usage

    pagoda.subtract.aspect(varinfo, aspect, center = TRUE)

### Arguments

`varinfo` | normalized variance info (from pagoda.varnorm())
`aspect` | a vector giving a cell-to-cell variation pattern that should be controlled for (length should be corresponding to ncol(varinfo$mat))
`center` | whether the matrix should be re-centered following pattern subtraction

### Value

a modified varinfo object with adjusted expression matrix (varinfo$mat)

### Examples

    data(pollen)
    cd <- clean.counts(pollen)

    knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=10, min.count.threshold=2, min.nonfailed=5, max.model.plots=10)
    varinfo <- pagoda.varnorm(knn, counts = cd, trim = 3/ncol(cd), max.adj.var = 5, n.cores = 1, plot = FALSE)
    # create go environment
    library(org.Hs.eg.db)
    # translate gene names to ids
    ids <- unlist(lapply(mget(rownames(cd), org.Hs.egALIAS2EG, ifnotfound = NA), function(x) x[1]))
    rids <- names(ids); names(rids) <- ids
    go.env <- lapply(mget(ls(org.Hs.egGO2ALLEGS), org.Hs.egGO2ALLEGS), function(x) as.character(na.omit(rids[x])))
    # clean GOs
    go.env <- clean.gos(go.env)
    # convert to an environment
    go.env <- list2env(go.env)
    # subtract the pattern
    cc.pattern <- pagoda.show.pathways(ls(go.env)[1:2], varinfo, go.env, show.cell.dendrogram = TRUE, showRowLabels = TRUE)  # Look at pattern from 2 GO annotations
    varinfo.cc <- pagoda.subtract.aspect(varinfo, cc.pattern)

[Package scde version 2.10.1 Index]