readSeastar {manta} | R Documentation

## Read SEAStAR output format

### Description

This function reads Vaughn Iverson's SEAStAR tabular format output and appends headers to it.

### Usage

    readSeastar(path,
    clmn.names=c('seq_id','bit_score','read_count','raw_abundance','fractional_abundance','mean_coverage','mean_read_length','seq_len','gc_percent','ref_seq_name','ref_seq_desc'),
    clmn.class = c("character", rep("numeric", 6), "integer", "numeric", rep("character", 2)),
    name.clmn='seq_id', ret.df=FALSE, ret.clmn='read_count', ct.calc=expression(raw_abundance*seq_len), header = FALSE, ...)

### Arguments

`path` | Path to the seastar file
`clmn.names` | The feild names for the absent header column
`clmn.class` | The class types for each of the columns
`name.clmn` | the seastar column to be used to name the rows of the dataframe
`ret.df` | Return the entire dataframe rather than just the calculated count column
`ret.clmn` | If ret.df is FALSE, return just this column as a vector. Can be 'count' as calculated by 'ct.calc'
`ct.calc` | the equation to use to calculate the counts
`header` | If the seastar tables have headers
`...` | Additional parameters passed on to read.delim

### Value

a SEAStAR formated matrix of per-reference/contig/gene stats (including counts)

### See Also

seastar2counts

### Examples

    conditions <- c('ambient','plusFe')
    ss.names <- caroline::nv(paste('Pgranii-',conditions,'.seastar', sep=''), conditions)

    ss.paths <- system.file("extdata",ss.names, package="manta")

    df <- readSeastar(ss.paths[1])

[Package manta version 1.26.0 Index]