filterBinMSnSet {pRoloc} | R Documentation

## Filter a binary MSnSet

### Description

Removes columns or rows that have a certain proportion or absolute number of 0 values.

### Usage

    filterBinMSnSet(object, MARGIN = 2, t, q, verbose = TRUE)

### Arguments

`object` | An `MSnSet`
`MARGIN` | 1 or 2. Default is 2.
`t` | Rows/columns that have `t` or less `1`s, it will be filtered out. When `t` and `q` are missing, default is to use `t = 1`.
`q` | If a row has a higher quantile than defined by `q`, it will be filtered out.
`verbose` | A `logical` defining of a message is to be printed. Default is `TRUE`.

### Value

A filtered `MSnSet`.

### Author(s)

Laurent Gatto

### See Also

`zerosInBinMSnSet`, `filterZeroCols`, `filterZeroRows`.

### Examples

    set.seed(1)
    m <- matrix(sample(0:1, 25, replace=TRUE), 5)
    m[1, ] <- 0
    m[, 1] <- 0
    rownames(m) <- colnames(m) <- letters[1:5]
    fd <- data.frame(row.names = letters[1:5])
    x <- MSnSet(exprs = m, fData = fd, pData = fd)
    exprs(x)
    ## Remove columns with no 1s
    exprs(filterBinMSnSet(x, MARGIN = 2, t = 0))
    ## Remove columns with one 1 or less
    exprs(filterBinMSnSet(x, MARGIN = 2, t = 1))
    ## Remove columns with two 1s or less
    exprs(filterBinMSnSet(x, MARGIN = 2, t = 2))
    ## Remove columns with three 1s
    exprs(filterBinMSnSet(x, MARGIN = 2, t = 3))
    ## Remove columns that have half or less of 1s
    exprs(filterBinMSnSet(x, MARGIN = 2, q = 0.5))

[Package pRoloc version 1.22.2 Index]