Package 'pgxRpi'

Title: R wrapper for Progenetix
Description: The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.
Authors: Hangjia Zhao [aut, cre] , Michael Baudis [aut]
Maintainer: Hangjia Zhao <[email protected]>
License: Artistic-2.0
Version: 1.3.0
Built: 2024-10-30 09:30:58 UTC
Source: https://github.com/bioc/pgxRpi

Help Index

A dataframe containing cytoband annotation details extracted from the hg19 gennome. It is used for CNV frequency visualization.

Description

A dataframe containing cytoband annotation details extracted from the hg19 gennome. It is used for CNV frequency visualization.

Usage

hg19_cytoband

Format

An object of class data.frame with 862 rows and 5 columns.

Value

cytoband of hg19 genome

Source

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz

A dataframe containing cytoband annotation details extracted from the hg38 gennome. It is used for CNV frequency visualization.

Description

A dataframe containing cytoband annotation details extracted from the hg38 gennome. It is used for CNV frequency visualization.

Usage

hg38_cytoband

Format

An object of class data.frame with 862 rows and 5 columns.

Value

cytoband of hg38 genome

Source

http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz

Query available filters

Description

This function retrieves available filters in the Progenetix database via the Beacon v2 API.

Usage

pgxFilter(
  prefix = NULL,
  return_all_prefix = FALSE,
  domain = "http://progenetix.org",
  entry_point = "beacon"
)

Arguments

prefix

A string specifying the prefix of filters, such as 'NCIT'. Default is NULL, which means that all available filters will be returned. When specified, it returns all filters with the specified prefix.
return_all_prefix

A logical value determining whether to return all valid prefixes of filters used in database. If TRUE, the prefix parameter will be ignored. Default is FALSE.
domain

A string specifying the domain of the query data resource. Default is "http://progenetix.org".
entry_point

A string specifying the entry point of the Beacon v2 API. Default is "beacon", resulting in the endpoint being "http://progenetix.org/beacon".

Value

Filter terms used in the data resource that you query.

Examples

pgxFilter(prefix = "NCIT")

Plot CNV frequency data

Description

Thie function plots the frequency of deletions and duplications

Usage

pgxFreqplot(
  data,
  chrom = NULL,
  layout = c(1, 1),
  filters = NULL,
  circos = FALSE,
  assembly = "hg38"
)

Arguments

data

CNV frequency object returned by the pgxLoader or segtoFreq functions.
chrom

A vector specifying which chromosomes to plot. If NULL, the plot will cover the entire genome. If specified, the frequencies are plotted with one panel for each chromosome. Default is NULL.
layout

Number of columns and rows in plot. Only used in plot by chromosome. Default is c(1,1).
filters

Index or string value indicating which filter to plot. The length of filters is limited to one if the parameter circos is FALSE. Default is the first filter.
circos

A logical value indicating whether to return a circos plot. If TRUE, it returns a circos plot that can display and compare multiple filters. Default is FALSE.
assembly

A string specifying the genome assembly version to apply to CNV frequency plotting. Allowed options are "hg19" and "hg38". Default is "hg38".

Value

The binned CNV frequency plot

Examples

## load necessary data (this step can be skipped in real implementation)
data("hg38_cytoband")
## get frequency data
freq <- pgxLoader(type="cnv_frequency", output ='pgxfreq', filters="NCIT:C3512")
## visualize
pgxFreqplot(freq)

Load data from Progenetix database via the Beacon v2 API with some extensions

Description

This function loads various data from Progenetix database via the Beacon v2 API with some extensions (BeaconPlus).

Usage

pgxLoader(
  type = NULL,
  output = NULL,
  biosample_id = NULL,
  individual_id = NULL,
  filters = NULL,
  limit = 0,
  skip = NULL,
  dataset = NULL,
  codematches = FALSE,
  save_file = FALSE,
  filename = "variant",
  num_cores = 1,
  domain = "http://progenetix.org",
  entry_point = "beacon"
)

Arguments

type

A string specifying output data type. Available options are "biosamples", "individuals", "analyses", "g_variants", "cnv_frequency", "cnv_fraction", and "sample_count". The options "biosamples", "individuals", and "analyses" return corresponding information. "g_variants" returns variants data. The options "cnv_frequency", "cnv_fraction" and "sample_count" are based on data in Progenetix, returning precomputed CNV frequency, CNV fraction per sample, and the count of samples for the given filter, respectively.
output

A string specifying output data format. The available options depend on the type parameter. When type is "g_variants", available options are NULL (default), "pgxseg", or "seg"; When type is "cnv_frequency", available options are "pgxfreq" or "pgxmatrix"; when type is "cnv_fraction", available options are NULL (default) or "pgxmatrix".
biosample_id

Identifiers used in the query database for identifying biosamples.
individual_id

Identifiers used in the query database for identifying individuals.
filters

Identifiers used in public repositories, bio-ontology terms, or custom terms such as c("NCIT:C7376", "PMID:22824167"). When multiple filters are used, they are combined using AND logic when the parameter type is "biosamples", "individuals", or "analyses"; OR logic when the parameter type is "cnv_frequency" or "sample_count".
limit

Integer to specify the number of returned profiles. Default is 0 (return all).
skip

Integer to specify the number of skipped profiles. E.g. if skip = 2, limit=500, the first 2*500 =1000 profiles are skipped and the next 500 profiles are returned. Default is NULL (no skip).
dataset

A string specifying the dataset to query from the Beacon response. Default is NULL, which includes results from all datasets.
codematches

A logical value determining whether to exclude samples from child concepts of specified filters in the ontology tree. If TRUE, only samples exactly matching the specified filters will be included. Do not use this parameter when filters include ontology-irrelevant filters such as PMID and cohort identifiers. Default is FALSE.
save_file

A logical value determining whether to save variant data as a local file instead of direct return. Only used when the parameter type is "g_variants". Default is FALSE.
filename

A string specifying the path and name of the file to be saved. Only used if the parameter save_file is TRUE. Default is "variants" in current work directory.
num_cores

Integer to specify the number of cores used for the variant query. Only used when the parameter type is "g_variants". Default is 1.
domain

A string specifying the domain of the query data resource. Default is "http://progenetix.org".
entry_point

A string specifying the entry point of the Beacon v2 API. Default is "beacon", resulting in the endpoint being "http://progenetix.org/beacon".

Value

Data from Progenetix database

Examples

## query metadata
biosamples <- pgxLoader(type="biosamples", filters = "NCIT:C3512")
## query variants
seg <- pgxLoader(type="g_variants", biosample_id = "pgxbs-kftvgx4y")
## query CNV frequency
freq <- pgxLoader(type="cnv_frequency", output ='pgxfreq', filters="NCIT:C3512")

Plot survival data of individuals

Description

This function provides the survival plot from individual metadata.

Usage

pgxMetaplot(data, group_id, condition, return_data = FALSE, ...)

Arguments

data

The data frame returned by the pgxLoader function, containing survival data for individuals. The survival state is represented by Experimental Factor Ontology in the "followup_state_id" column, and the survival time is represented in ISO 8601 duration format in the "followup_time" column.
group_id

A string specifying which column is used for grouping in the Kaplan-Meier plot.
condition

A string for splitting individuals into younger and older groups, following the ISO 8601 duration format. Only used if group_id is "age_iso".
return_data

A logical value determining whether to return the metadata used for plotting. Default is FALSE.
...

Other parameters relevant to KM plot. These include pval, pval.coord, pval.method, conf.int, linetype, and palette (see ggsurvplot from survminer)

Value

The KM plot from input data

Examples

individuals <- pgxLoader(type="individuals",filters="NCIT:C3512")
pgxMetaplot(individuals, group_id="age_iso", condition="P65Y")

Extract, analyse and visualize "pgxseg" files

Description

This function extracts segment variants, CNV frequency, and metadata from local "pgxseg" files and supports survival data visualization.

Usage

pgxSegprocess(
  file,
  group_id = "group_id",
  show_KM_plot = FALSE,
  return_metadata = FALSE,
  return_seg = FALSE,
  return_frequency = FALSE,
  assembly = "hg38",
  cnv_column_idx = 6,
  bin_size = 1e+06,
  overlap = 1000,
  soft_expansion = 0.1,
  ...
)

Arguments

file

A string specifying the path and name of the "pgxseg" file where the data is to be read.
group_id

A string specifying which id is used for grouping in KM plot or CNV frequency calculation. Default is "group_id".
show_KM_plot

A logical value determining whether to return the Kaplan-Meier plot based on metadata. Default is FALSE.
return_metadata

A logical value determining whether to return metadata. Default is FALSE.
return_seg

A logical value determining whether to return segment data. Default is FALSE.
return_frequency

A logical value determining whether to return CNV frequency data. The frequency calculation is based on segments in segment data and specified group id in metadata. Default is FALSE.
assembly

A string specifying the genome assembly version to apply to CNV frequency calculation and plotting. Allowed options are "hg19" and "hg38". Default is "hg38".
cnv_column_idx

Index of the column specifying the CNV state used for calculating CNV frequency. The index must be at least 6, with the default set to 6. The CNV states should either contain "DUP" for duplications and "DEL" for deletions, or level-specific CNV states represented using Experimental Factor Ontology (EFO) codes.
bin_size

Size of genomic bins used in CNV frequency calculation to split the genome, in base pairs (bp). Default is 1,000,000.
overlap

Numeric value defining the amount of overlap between bins and segments considered as bin-specific CNV, in base pairs (bp). Default is 1,000.
soft_expansion

Fraction of bin_size to determine merge criteria. During the generation of genomic bins, division starts at the centromere and expands towards the telomeres on both sides. If the size of the last bin is smaller than soft_expansion * bin_size, it will be merged with the previous bin. Default is 0.1.
...

Other parameters relevant to KM plot. These include pval, pval.coord, pval.method, conf.int, linetype, and palette (see ggsurvplot from survminer)

Value

Segments data, CNV frequency object, meta data or KM plots from local "pgxseg" files

Examples

file_path <- system.file("extdata", "example.pgxseg",package = 'pgxRpi')
info <- pgxSegprocess(file=file_path,show_KM_plot = TRUE, return_seg = TRUE, return_metadata = TRUE)

Calculate CNV frequency data from given segment data

Description

Thie function calculates the frequency of deletions and duplications

Usage

segtoFreq(
  data,
  cnv_column_idx = 6,
  cohort_name = "unspecified cohort",
  assembly = "hg38",
  bin_size = 1e+06,
  overlap = 1000,
  soft_expansion = 0.1
)

Arguments

data

Segment data containing CNV states. The first four columns should represent sample ID, chromosome, start position, and end position, respectively. The fifth column can contain the number of markers or other relevant information. The column representing CNV states (with a column index of 6 or higher) should either contain "DUP" for duplications and "DEL" for deletions, or level-specific CNV states such as "EFO:0030072", "EFO:0030071", "EFO:0020073", and "EFO:0030068", which correspond to high-level duplication, low-level duplication, high-level deletion, and low-level deletion, respectively.
cnv_column_idx

Index of the column specifying the CNV state. Default is 6, based on the "pgxseg" format used in Progenetix. If the input segment data follows the general .seg file format, this index may need to be adjusted accordingly.
cohort_name

A string specifying the cohort name. Default is "unspecified cohort".
assembly

A string specifying the genome assembly version for CNV frequency calculation. Allowed options are "hg19" or "hg38". Default is "hg38".
bin_size

Size of genomic bins used to split the genome, in base pairs (bp). Default is 1,000,000.
overlap

Numeric value defining the amount of overlap between bins and segments considered as bin-specific CNV, in base pairs (bp). Default is 1,000.
soft_expansion

Fraction of bin_size to determine merge criteria. During the generation of genomic bins, division starts at the centromere and expands towards the telomeres on both sides. If the size of the last bin is smaller than soft_expansion * bin_size, it will be merged with the previous bin. Default is 0.1.

Value

The binned CNV frequency stored in "pgxfreq" format

Examples

## load necessary data (this step can be skipped in real implementation)
data("hg38_cytoband")
## get pgxseg data
seg <- read.table(system.file("extdata", "example.pgxseg",package = 'pgxRpi'),header=TRUE,sep = "\t")
## calculate frequency data
freq <- segtoFreq(seg)
## visualize
pgxFreqplot(freq)