get_pav_obj: get_pav_obj

In SJTU-CGM/vPanG: An R package to analyze and visualize PAV results from pan-genome of "map-to-pan" strategy.

Description

Get an object of the PAV class.

Usage

get_pav_obj(
  pav_data,
  phen_info = NULL,
  gene_info = NULL,
  add_softcore = T,
  add_private = T,
  softcore_loss_rate = 0.1,
  softcore_p_value = 0.05
)

Arguments

pav_data	A numeric 'matrix' or 'data.frame' of PAV data. '0' represent "absence" and '1' represent "presence". The row names are gene names. The column names are sample names.
phen_info	The phenotype data. The row names are sample name.
gene_info	The gene data. The row names are gene name.
add_softcore	A logical value indicating whether to consider 'soft-core' when determining the gene types.
add_private	A logical value indicating whether to consider 'private' when determining the gene types.
softcore_loss_rate	A numeric vector of loss rate.
softcore_p_value	A numeric vector of p-value (binomial test). 'add_softcore' and 'add_private' are logical values indicating whether to consider "softcore" and "private" when determining the gene types. If 'add_softcore' is 'TRUE', the genes with loss rates not significantly larger than 'softcore_loss_rate' will be considered as "softcore" gene. Binomial tests (with a null hypothesis of loss rate < 'softcore_loss_rate') are carried out for each gene. A p-vlaue below 'softcore_p_value' means that this gene is lost in a significant proportion and is a distributed gene(loss rate > 'softcore_loss_rate'). If 'add_private' is 'TRUE', the genes present in only one sample will be condidered as "private" gene.

SJTU-CGM/vPanG documentation built on Dec. 18, 2021, 11:59 a.m.