readSeastar: Read SEAStAR output format

In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

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])
  

armbrustlab/manta documentation built on Dec. 17, 2019, 12:06 a.m.