process_cnvkit | R Documentation |
For more information read: https://cnvkit.readthedocs.io/en/stable/pipeline.html
process_cnvkit(
target = build_default_reference_list()$HG19$panel$PCF_V3$binned$target,
antitarget = build_default_reference_list()$HG19$panel$PCF_V3$binned$antitarget,
ref_genome = build_default_reference_list()$HG19$reference$genome,
access = build_default_reference_list()$HG19$reference$access_5k,
sif_cnvkit = build_default_sif_list()$sif_cnvkit,
pon = build_default_reference_list()$HG19$panel$PCF_V3$variant$pon_cn_male,
bam = NULL,
patient_id = NULL,
seg_method = "cbs",
seq_method = "hybrid",
diagram = TRUE,
scatter = TRUE,
read_count = FALSE,
min_mapq = 0,
gc = TRUE,
edge = TRUE,
rmask = TRUE,
smooth = FALSE,
drop_low_coverage = TRUE,
drop_outliers = 10,
range_scatter = NULL,
range_list_scatter = NULL,
genes_scatter = NULL,
margin_width_scatter = 1e+06,
plot_by_bin_scatter = FALSE,
trend_scatter = FALSE,
antitarget_symbol_scatter = "@",
segment_colour_scatter = "red",
y_max_scatter = NULL,
y_min_scatter = NULL,
cn_thr_diagram = 0.5,
min_probes_diagram = 3,
male_reference_diagram = FALSE,
gender_diagram = "male",
shift_diagram = TRUE,
...
)
ref_genome |
REQUIRED Path to reference genome fasta file. |
access |
OPTIONAL Path to reference genome accessibility. Default none |
sif_cnvkit |
REQUIRED Path to cnvkit sif file. |
pon |
OPTIONAL Path to panel of normal. |
seg_method |
OPTIONAL Method to use to generate segmentation calls.Default cbs. Options "cbs","flasso","haar","none","hmm","hmm-tumor","hmm-germline" |
seq_method |
OPTIONAL Sequenced methods used. Default hybrid. Options "hybrid","amplicon","wgs" |
range_scatter |
OPTIONAL Range to show in chr:start-end format. Default none |
range_list_scatter |
OPTIONAL Path to BED file with range list. Default none |
genes_scatter |
OPTIONAL List of genes to focus on. Default none. |
margin_width_scatter |
OPTIONAL Default gene margin width. Default 1000000 |
plot_by_bin_scatter |
OPTIONAL Assume all bins are the same size. Default FALSE |
trend_scatter |
OPTIONAL Show trendline. Default TRUE. |
antitarget_symbol_scatter |
OPTIONAL Show antitarget probes with this symbol. Default "@" |
segment_colour_scatter |
OPTIONAL Show antitarget probes with this symbol. Default "@" |
y_max_scatter |
OPTIONAL Y max range. Default NULL. |
y_min_scatter |
OPTIONAL Y min range. Default NULL. |
cn_thr_diagram |
OPTIONAL Copy number threshold. Default 0.5 |
min_probes_diagram |
OPTIONAL Minimum number of probes to show a gene. Default 3 |
male_reference_diagram |
OPTIONAL Assume inputs were normalized to a male reference. Default FALSE |
gender_diagram |
OPTIONAL Assume sample gender. Default male |
shift_diagram |
OPTIONAL Adjust the X and Y chromosomes according to sample sex. Default TRUE |
tumour |
REQUIRED Path to tumour BAM file. |
normal |
OPTIONAL Path to normal BAM file. |
rdata |
OPTIONAL Import R data information with list of BAM. |
selected |
OPTIONAL Select BAM from list. |
output_name |
OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used. |
output_dir |
OPTIONAL Path to the output directory. |
normal_ichor |
OPTIONAL Path to normal samples. Default c(0.5,0.6,0.7,0.8,0.9) |
ploidy_ichor |
OPTIONAL Initial tumour ploidy; can be more than one value if additional ploidy initializations are desired. Default: 2 |
lambda_ichor |
OPTIONAL Initial Student's t precision; must contain 4 values (e.g. c(1500,1500,1500,1500)); if not provided then will automatically use based on variance of data |
scStates_ichor |
OPTIONAL Subclonal states to consider. Default NULL |
output_name_ichor |
OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used. |
lambdaScaleHyperParam_ichor |
OPTIONAL Hyperparameter (scale) for Gamma prior on Student's-t precision. Default 3 |
maxCN_ichor |
OPTIONAL Total clonal states. Default 7. |
estimateNormal_ichor |
OPTIONAL Estimate normal. Default TRUE. |
estimateScPrevalence_ichor |
OPTIONAL Estimate subclonal prevalence. Default TRUE. |
estimatePloidy_ichor |
OPTIONAL Estimate tumour ploidy. Default TRUE. |
maxFracGenomeSubclone_ichor |
OPTIONAL Exclude solutions with subclonal genome fraction greater than this value. Default 0.5 |
maxFracCNASubclone_ichor |
OPTIONAL Exclude solutions with fraction of subclonal events greater than this value. Default 0.7 |
minSegmentBins_ichor |
OPTIONAL Minimum number of bins for largest segment threshold required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction |
altFracThreshold_ichor |
OPTIONAL Minimum proportion of bins altered required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction. Default: 0.05 |
includeHOMD_ichor |
OPTIONAL If FALSE, then exclude HOMD state. Useful when using large bins (e.g. 1Mb). Default FALSE. |
txnE_ichor |
OPTIONAL Self-transition probability. Increase to decrease number of segments. Default: 0.9999999 |
txnStrength_ichor |
OPTIONAL Transition pseudo-counts. Exponent should be the same as the number of decimal places of –txnE. Default: 1e+07 |
plotFileType_ichor |
OPTIONAL File format for output plots. Default pdf |
plotYLim_ichor |
OPTIONAL ylim to use for chromosome plots. Default: c(-2,2) |
threads |
OPTIONAL Number of threads to split the work. Default 4 |
ram |
OPTIONAL RAM memory to asing to each thread. Default 4 |
verbose |
OPTIONAL Enables progress messages. Default False. |
mode |
REQUIRED Where to parallelize. Default local. Options "local","batch" |
executor_id |
Task EXECUTOR ID. Default "recalCovariates" |
task_name |
Task name. Default "recalCovariates" |
time |
OPTIONAL If batch mode. Max run time per job. Default "48:0:0" |
update_time |
OPTIONAL If batch mode. Job update time in seconds. Default 60. |
wait |
OPTIONAL If batch mode wait for batch to finish. Default FALSE |
hold |
OPTIONAL HOld job until job is finished. Job ID. |
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