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: 1.1.4
Built: 2024-07-25 03:03:47 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

Count samples in one collation of a given filter

Description

This function returns the number of samples for every filter in Progenetix database.

Usage

pgxCount(
  filters = NULL,
  domain = "http://progenetix.org",
  dataset = "progenetix"
)

Arguments

filters

A single or a comma-concatenated list of identifiers such as c("NCIT:C7376","icdom-98353")
domain

A string specifying the domain of database. Default is "http://progenetix.org".
dataset

A string specifying the dataset to query. Default is "progenetix". Other available options are "cancercelllines".

Value

Count of samples in the given filter

Examples

pgxCount(filters = "NCIT:C3512")

Query available filters

Description

This function retrieves available filters in the Progenetix database.

Usage

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

Arguments

prefix

A string specifying the prefix of filters, such as 'NCIT' and 'PMID'. 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 Progenetix. If TRUE, the prefix parameter will be ignored. Default is FALSE.
domain

A string specifying the domain of the Progenetix database. Default is "http://progenetix.org".
dataset

A string specifying the dataset to query. Default is "progenetix". Other available options are "cancercelllines".

Value

filter terms used in Progenetix.

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,
  highlight = NULL,
  assembly = "hg38"
)

Arguments

data

The frequency object returned by pgxLoader function.
chrom

A vector with chromosomes to be plotted. If NULL, return the plot by 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 to indicate which filter to be plotted, such as 1 (the first filters in data slot of object ) or 'NCIT:C4038' (specific filter name). The length of filters is limited to one if the parameter circos is False. Default is 1.
circos

A logical value to indicate if return a circos plot. If TRUE, it can return a circos plot with multiple filters for display and comparison. Default is FALSE.
highlight

Indices of genomic bins to be highlighted with red color.
assembly

A string specifying which genome assembly version should be applied to CNV frequency plotting. Allowed options are "hg19", "hg38". Default is "hg38" (genome version used in Progenetix).

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="frequency", output ='pgxfreq', filters="NCIT:C3512")
## visualize
pgxFreqplot(freq)

Load data from Progenetix database

Description

This function loads various data from Progenetix database.

Usage

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

Arguments

type

A string specifying output data type. Available options are "biosample", "individual", "variant" or "frequency". The first two options return corresponding metadata, "variant" returns CNV variant data, and "frequency" returns precomputed CNV frequency based on data in Progenetix.
output

A string specifying output data format. When the parameter type is "variant", available options are NULL, "pgxseg", "seg", "coverage", or "pgxmatrix"; When the parameter type is "frequency", available options are "pgxfreq" or "pgxmatrix".
filters

Identifiers for cancer type, literature, cohorts, and age such as c("NCIT:C7376", "pgx:icdom-98353", "PMID:22824167", "pgx:cohort-TCGAcancers", "age:>=P50Y").
codematches

A logical value determining whether to exclude samples from child concepts of specified filters that belong to cancer type/tissue encoding system (NCIt, icdom/t, Uberon). If TRUE, retrieved samples only keep samples exactly encoded by specified filters. Do not use this parameter when filters include ontology-irrelevant filters such as PMID and cohort identifiers. Default is FALSE.
filterLogic

A string specifying logic for combining multiple filters when query metadata (the paramter type = "biosample" or "individual"). Available options are "AND" and "OR". Default is "AND". An exception is filters associated with age that always use AND logic when combined with any other filter, even if filterLogic = "OR", which affects other filters. Note that when type = "frequency", the combining logic is "OR", which is not changed by this parameter.
limit

Integer to specify the number of returned biosample/individual/variant profiles for each filter. Default is 0 (return all).
skip

Integer to specify the number of skipped biosample/individual/variant profiles for each filter. 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).
biosample_id

Identifiers used in Progenetix database for identifying biosamples.
individual_id

Identifiers used in Progenetix database for identifying individuals.
save_file

A logical value determining whether to save the segment variant data as file instead of direct return. Only used when the parameter type is "variant" and output is "pgxseg" or "seg". 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.seg/pgxseg" 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 "variant". Default is 1.
domain

A string specifying the domain of database. Default is "http://progenetix.org".
dataset

A string specifying the dataset to query. Default is "progenetix". Other available options are "cancercelllines".

Value

Data from Progenetix database

Examples

## query metadata
biosamples <- pgxLoader(type="biosample", filters = "NCIT:C3512")
## query segment variants
seg <- pgxLoader(type="variant", output = "pgxseg", biosample_id = "pgxbs-kftvgx4y")
## query CNV frequency
freq <- pgxLoader(type="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 meatdata of individuals returned by pgxLoader function.
group_id

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

Condition for splitting individuals into younger and older groups. Only used if group_id is age related.
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="individual",filters="NCIT:C3512")
pgxMetaplot(individuals, group_id="age_iso", condition="P65Y")

Extract, analyse and visualize "pgxseg" files

Description

This function extracts segments, 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",
  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 which genome assembly version should be applied to CNV frequency calculation and plotting. Allowed options are "hg19", "hg38". Default is "hg38".
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 with CNV states. The first four columns should specify sample ID, chromosome, start position, and end position, respectively. The column representing CNV states should contain either "DUP" for duplications or "DEL" for deletions.
cnv_column_idx

Index of the column specifying CNV state. Default is 6, following the "pgxseg" format used in Progenetix. If the input segment data uses the general .seg file format, it might need to be set differently.
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)
## calculate frequency data
freq <- segtoFreq(seg)
## visualize
pgxFreqplot(freq)