RNAseqCNV_wrapper: RNAseqCNV_wrapper

In honzee/RNAseqCNV: A package for CNV analysis from RNA-seq data in B-cell acute lymphoblastic leukaemia

RNAseqCNV_wrapper

Description

Wrapper for generating figures and tables for CNV estimation from RNA-seq

Usage

RNAseqCNV_wrapper(
  config,
  metadata,
  snv_format,
  adjust = TRUE,
  arm_lvl = TRUE,
  estimate_lab = TRUE,
  genome_version = "hg38",
  gene_annotation = NULL,
  SNP_to_keep = NULL,
  par_regions = NULL,
  centromeric_regions = NULL,
  weight_tab = weight_table,
  generate_weights = FALSE,
  model_gend = model_gender,
  model_dip = model_dipl,
  model_alter = model_alt,
  model_alter_noSNV = model_noSNV,
  batch = FALSE,
  standard_samples = NULL,
  CNV_matrix = FALSE,
  scale_cols = scaleCols,
  dpRatioChromEdge = dpRatioChrEdge,
  minDepth = 20,
  mafRange = c(0.05, 0.9),
  minReadCnt = 3,
  samp_prop = 0.8,
  weight_samp_prop = 1
)

Arguments

config	path to R script assigning paths to needed directories into variables: 1. count_dir - path to a directory with count files, 2. snv_dir - path to a directory with files with snv information (either vcf or custom tabular data), out_dir - path to an output directory. More detailed description can be found in the package README file.
metadata	path to a metadata table with three columns. First colum: sample names, second column: file names of count files, third column: file names of snv files. There should be no header. More information is included in the package README file.
snv_format	character string, either "vcf" or "custom". "vcf" argument should be used when vcf files with snv information are generated with GATK. Otherwise "custom" arguments can be used when input with snv iformation has 4 required columns: chromosome, locus of the snv, overall sequencing depth of the locus and MAF. MAF is the proportion of alternative allele sequencing depth to overall sequencing depth of the locus.
adjust	logical value, If TRUE, expression is centered according to the random forest estimated diploid chromosomes. Default = TRUE.
arm_lvl	logical value, If TRUE, arm_lvl figures will be printed (increases run-time significantly). Defaul = TRUE.
estimate_lab	logical value, If TRUE, CNV estimation labels will be included in the final figure.
genome_version	character string, either "hg19" or "hg38" (default). The gene annotation, kept SNPs, pseudoautosomal regions and centromeric regions will be selected accordingly to the the chosen version. If the information is supplied by the user by any of these arguments - referData, keptSNP, par_region, centr_refer, the internal data will be overwritten.
gene_annotation	table, reference data for gene annotation with ensamble ids
SNP_to_keep	vector of realiable SNPs to keep for the MAF graphs
par_regions	table with pseudoautosomal regions. These regions will be filtered out.
centromeric_regions	table with chromosomal centromeric locations.
weight_tab	table with per-gene weight for calculating weighted quantiles for the boxplots in the main figure.
generate_weights	logical value, if TRUE, weights for calculating weighted quantiles will be contructed from variance and depth of the analyzed cohort of samples. If batch is TRUE, the weights will be analyzed from the batch of input samples, if FALSE the weight will be generate from joined diploid standard and analyzed sample.
model_gend	random forest model for estimating gender based on the expression of certain genes on chromosome Y.
model_dip	random forest model for estimating whether chromosome arm is diploid.
model_alter	random forest model for estimating the CNVs on chromosome arm.
model_alter_noSNV	random forest model for estimating CNVs on chromosome arm level in case not enough SNV information is available to conctruct MAF density curve.
batch	logical value, if TRUE, the samples will be normalized together as a batch, also gene expression median will be calculated from these samples
standard_samples	character vector with sample names of samples which should be used as a standard for vst and log2 fold centering. The samples names must be included in the metadata table and batch analysis cannot be TRUE. If NULL (default), in-build standard samples will be used.
CNV_matrix	logical value, if TRUE, additional matrix of called CNVs for all analyzed samples will be output
scale_cols	colour scaling for box plots according to the median of a boxplot.
minDepth	minimal depth of of SNV to be kept (default 20).
mafRange	numeric value, two numerical values specifying the range of MAFs of SNVs to be kept (default c(0.05, 0.9))
minReadCnt	numeric value value used for filtering genes with low expression according to to formula: at least samp_prop*100 percent of samples have more reads than minReadCnt. (default 3)
samp_prop	sample proportion which is required to have at least minReadCnt reads for a gene. The samples inlcude the diploid reference (from standard_samples parameter) and analyzed sample. (default 0.8)
weight_samp_prop	proportion of samples with highest weight to be kept. default (1)
dpRationChromEdge	table with chromosome start and end base positions.

honzee/RNAseqCNV documentation built on Jan. 30, 2024, 7:07 p.m.