manta (version 1.18.0)

readSeastar: 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])