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File descriptions

Source: vignettes/descriptions.Rmd
descriptions.Rmd

List of output files

Numbat generates a number of files in the output folder. The file names are post-fixed with the ith iteration of phylogeny optimization. Here is a detailed list:

Analysis results
  • bulk_subtrees_{i}.tsv.gz: Subtree pseudobulk profiles based on current cell lineage tree
  • segs_consensus_{i}.tsv.gz: Consensus segments from subtree pseudobulk HMMs
  • bulk_clones_{i}.tsv.gz: Clone-level pseudobulk profiles based on current cell lineage tree
  • exp_post_{i}.tsv: Expression-based posterior probabilities of CNV states for each segment in each cell.
  • allele_post_{i}.tsv: Allele-based posterior probabilities of CNV states for each segment in each cell.
  • joint_post_{i}.tsv: Joint posterior probabilities of CNV states for each segment in each cell.
  • clone_post_{i}.tsv: Single-cell clone assignment and tumor versus normal classification posteriors
  • bulk_clones_final.tsv.gz: Clone-level pseudobulk profiles based on final cell lineage tree
  • bulk_subtrees_retest_{i}.tsv.gz: Subtree pseudobulk profiles after retesting CNV states
  • gexp_roll_wide.tsv.gz: window-smoothed normalized expression profiles of single cells
  • segs_loh.tsv: Clonal LoH segments; written if call_clonal_loh is enabled
Plots
  • exp_roll_clust.png: visualization of single-cell smoothed gene expression profiles
  • bulk_subtrees_{i}.png: visualization of subtree pseudobulk CNV profiles
  • bulk_clones_{i}.png: visualization of clone pseudobulk CNV profiles
  • bulk_clones_final.png: visualization of final clone pseudobulk CNV profiles
  • tree_list_{i}.rds: list of candidate phylogeneies in the maximum likelihood tree search
  • panel_{i}.png: integrated visualization of single-cell phylogeny and CNV landscape
Lineage trees
  • hc.rds: initial hierarchical clustering result based on smoothed expression
  • clones_{i}.rds: list of candidate clones used to generate bulk_clones_{i}.tsv.gz
  • subtrees_{i}.rds: list of candidate subtrees used to generate bulk_subtrees_{i}.tsv.gz
  • tree_NJ_{i}.rds: neighbor joining tree
  • mut_graph_{i}.rds: mutation graph derived from the current cell lineage tree
  • tree_ML_{i}.rds: maximum likelihood tree (in ape::phylo format)
  • tree_final_{i}.rds: final cell lineage tree with mutation and clone annotation (in tbl_graph format)
Misc
  • log.txt: log file
  • sc_refs.rds: list of best reference match for each cell

Single-cell posteriors

cell: character; Cell barcode

CHROM: character; Chromosome

seg: character; Segment ID

cnv_state: character; CNV state estimated from pseudobulk HMM

n_snp: numeric; Number of SNPs in segment

seg_start: numeric; Segment start position

seg_end: numeric; Segment end position

n_genes: numeric; Number of genes in segment

n_snps: numeric; Number of SNPs in segment

prior_loh: numeric; Prior probability of CNLoH

prior_amp: numeric; Prior probability of amplification

prior_del: numeric; Prior probability of deletion

prior_bamp: numeric; Prior probability of biallelic amplification

prior_bdel: numeric; Prior probability of biallelic deletion

l11_x: numeric; Log-likelihood of CNV state 1:1 (neutral) given expression data

l20_x: numeric; Log-likelihood of CNV state 2:0 (CNLoH) given expression data

l10_x: numeric; Log-likelihood of CNV state 1:0 (deletion) given expression data

l21_x: numeric; Log-likelihood of CNV state 2:1 (amplification) given expression data

l31_x: numeric; Log-likelihood of CNV state 3:1 (amplification) given expression data

l22_x: numeric; Log-likelihood of CNV state 2:2 (biallelic amplification) given expression data

l00_x: numeric; Log-likelihood of CNV state 0:0 (biallelic deletion) given expression data

Z_cnv_x: numeric; Total log(likelihood * prior) of CNV states given expression data

Z_n_x: numeric; Total log(likelihood * prior) of neutral state given expression data

logBF_x: numeric; Log Bayes factor of CNV state vs. neutral state given expression data

l11_y: numeric; Log-likelihood of CNV state 1:1 (neutral) given allele data

l20_y: numeric; Log-likelihood of CNV state 2:0 (CNLoH) given allele data

l10_y: numeric; Log-likelihood of CNV state 1:0 (deletion) given allele data

l21_y: numeric; Log-likelihood of CNV state 2:1 (gain) given allele data

l31_y: numeric; Log-likelihood of CNV state 3:1 (amplification) given allele data

l22_y: numeric; Log-likelihood of CNV state 2:2 (biallelic amplification) given allele data

l00_y: numeric; Log-likelihood of CNV state 0:0 (biallelic deletion) given allele data

Z_cnv_y: numeric; Total log(likelihood * prior) of CNV states given allele data

Z_n_y: numeric; Total log(likelihood * prior) of neutral state given allele data

logBF_y: numeric; Log Bayes factor of CNV state vs. neutral state given allele data

LLR: numeric; Log-likelihood ratio of CNV state vs. neutral state

LLR_x: numeric; Log-likelihood ratio of CNV state vs. neutral state given expression data

LLR_y: numeric; Log-likelihood ratio of CNV state vs. neutral state given allele data

l11: numeric; Joint log-likelihood of CNV state 1:1 (neutral)

l20: numeric; Joint log-likelihood of CNV state 2:0 (CNLoH)

l10: numeric; Joint log-likelihood of CNV state 1:0 (deletion)

l21: numeric; Joint log-likelihood of CNV state 2:1 (amplification)

l31: numeric; Joint log-likelihood of CNV state 3:1 (amplification)

l22: numeric; Joint log-likelihood of CNV state 2:2 (biallelic amplification)

l00: numeric; Joint log-likelihood of CNV state 0:0 (biallelic deletion)

Z_amp: numeric; Total log(likelihood * prior) of amplification state

Z_loh: numeric; Total log(likelihood * prior) of CNLoH state

Z_del: numeric; Total log(likelihood * prior) of deletion state

Z_bamp: numeric; Total log(likelihood * prior) of biallelic amplification state

Z_bdel: numeric; Total log(likelihood * prior) of biallelic deletion state

Z_n: numeric; Total log(likelihood * prior) of neutral state

Z: numeric; Total log(likelihood * prior) of all states

Z_cnv: numeric; Total log(likelihood * prior) of CNV states

p_amp: numeric; Joint posterior probability of amplification states (2:1, 3:1)

p_neu: numeric; Joint posterior probability of neutral state

p_del: numeric; Joint posterior probability of deletion state

p_loh: numeric; Joint posterior probability of CNLoH state

p_bamp: numeric; Joint posterior probability of biallelic amplification state

p_bdel: numeric; Joint posterior probability of biallelic deletion state

logBF: numeric; Joint log Bayes factor of CNV state vs. neutral state

p_cnv: numeric; Joint posterior probability of CNV state

p_n: numeric; Joint posterior probability of neutral state

p_cnv_x: numeric; Joint posterior probability of CNV state given expression data

p_cnv_y: numeric; Joint posterior probability of CNV state given allele data

cnv_state_mle: character; Maximum likelihood CNV state

cnv_state_map: character; Maximum a posteriori CNV state

seg_label: character; Segment label

avg_entropy: numeric; Average entropy of CNV posterior in single cells

phi_mle: numeric; Maximum likelihood of total copy number ratio relative to diploid (phi)

mu: numeric; Mean of expression count distribution in the cell (Poisson log-Normal)

sigma: numeric; Standard deviation of expression count distribution in the cell (Poisson log-Normal)

ref: character; Best-matching single-cell expression reference

major: integer; Major allele count; total SNP pileup counts deriving from the major haplotype in the CNV region for the given cell

minor: integer; Minor allele count; total SNP pileup counts deriving from the minor haplotype in the CNV region for the given cell

total: integer; Total allele count

MAF: numeric; Major allele frequency

Pseudobulk profiles

snp_id: character; SNP ID

CHROM: character; Chromosome

POS: integer; Genomic position

cM: numeric; Genetic distance in cM

REF: character; Reference allele

ALT: character; Alternate allele

GT: character; Phased genotype

gene: character; Gene symbol

AD: integer; Allelic depth

DP: integer; Total depth

AR: numeric; Allelic fraction

snp_index: integer; SNP index

pBAF: numeric; Phased BAF

pAD: numeric; Phased allelic depth

inter_snp_cm: numeric; Genetic distance in cM between adjacent SNPs

p_s: numeric; Probability of phase switch based on inter-SNP distance

Y_obs: integer; Observed gene expression counts (the X/Y notation is switched here..)

lambda_obs: numeric; Observed gene expression magnitude

lambda_ref: numeric; Reference gene expression magnitude

d_obs: numeric; Total gene expression count in the cell

gene_start: integer; Gene start position

gene_end: integer; Gene end position

gene_length: integer; Gene length

gene_index: integer; Gene index

logFC: numeric; Log2 fold change of gene expression

lnFC: numeric; Natural log fold change of gene expression

mse: numeric; Mean squared error of logFC

snp_rate: numeric; SNP rate

loh: logical; True if segment has a clonal LoH (deletion)

n_cells: integer; Number of cells in the pseudobulk

members: character; Cell groups included in the pseudobulk

sample: character/integer; Sample ID

state: character; CNV state

boundary: logical; True if the marker is at CNV boundary

seg_start_index: integer; Segment start marker index

seg_end_index: integer; Segment end marker index

seg_start: integer; Segment start position

seg_end: integer; Segment end position

seg_length: integer; Segment length in bp

seg: character; Segment ID

seg_cons: character; Consensus segment ID

diploid: logical; True if the segment is diploid

mu: numeric; Mean of expression count distribution in the pseudobulk (Poisson log-Normal)

sig: numeric; Standard deviation of expression count distribution in the pseudobulk (Poisson log-Normal)

cnv_state: character; CNV state

n_genes: integer; Number of genes in the segment

n_snps: integer; Number of SNPs in the segment

theta_hat: numeric; Crude estimate haplotype frequency based on MAF

theta_mle: numeric; Maximum likelihood estimate of haplotype frequency (theta)

theta_sigma: numeric; Standard deviation of theta MLE

L_y_n: numeric; Neutral log-likelihood of allele data

L_y_d: numeric; Deletion log-likelihood of allele data

L_y_a: numeric; Amplification log-likelihood of allele data

phi_mle: numeric; Maximum likelihood of total copy number ratio relative to diploid (phi)

phi_sigma: numeric; Standard deviation of phi MLE

L_x_n: numeric; Neutral log-likelihood of expression data

L_x_d: numeric; Deletion log-likelihood of expression data

L_x_a: numeric; Amplification log-likelihood of expression data

Z_cnv: numeric; Total log(likelihood * prior) of CNV states

Z_n: numeric; Total log(likelihood * prior) of neutral state

Z: numeric; Total log(likelihood * prior) of all states

logBF: numeric; Joint log Bayes factor of CNV state vs. neutral state

p_neu: numeric; Joint posterior probability of neutral state

p_loh: numeric; Joint posterior probability of CNLoH state

p_amp: numeric; Joint posterior probability of amplification states (2:1, 3:1)

p_del: numeric; Joint posterior probability of deletion state

p_bamp: numeric; Joint posterior probability of biallelic amplification state

p_bdel: numeric; Joint posterior probability of biallelic deletion state

LLR_x: numeric; Log-likelihood ratio of expression data

LLR_y: numeric; Log-likelihood ratio of allele data

LLR: numeric; Log-likelihood ratio of all data

cnv_state_post: character; Maximum a posteriori (retest) CNV state

state_post: character; Maximum a posteriori CNV allelic state

p_up: numeric; HMM posterior probability of variant allele belonging to the major haplotype

haplo_post: numeric; Maximum a posteriori haplotype state assignment

haplo_naive: numeric; Naive haplotype state assignment (based on BAF)

major_count: integer; Major allele count; total SNP counts deriving from the major haplotype in the CNV region in the pseudobulk

minor_count: integer; Minor allele count; total SNP counts deriving from the minor haplotype in the CNV region in the pseudobulk

theta_hat_roll: numeric; Crude estimate haplotype frequency based on MAF (rolling window)

phi_mle_roll: numeric; Maximum likelihood of total copy number ratio relative to diploid (phi, rolling window)

nu: numeric; Phase-switch rate used in the HMM

gamma: numeric; Allele inverse-overdispersion used in the HMM

Consensus segments

consensus segments from subtree pseudobulk HMMs

sample: character/integer; Sample ID

CHROM: character; Chromosome

seg: character; Segment ID

cnv_state: character; CNV state

cnv_state_post: character; Maximum a posteriori (retest) CNV state

seg_start: integer; Segment start position

seg_end: integer; Segment end position

seg_start_index: integer; Segment start marker index

seg_end_index: integer; Segment end marker index

theta_mle: numeric; Maximum likelihood estimate of haplotype frequency (theta)

theta_sigma: numeric; Standard deviation of theta MLE

phi_mle: numeric; Maximum likelihood of total copy number ratio relative to diploid (phi)

phi_sigma: numeric; Standard deviation of phi MLE

p_loh: numeric; Joint posterior probability of CNLoH state

p_del: numeric; Joint posterior probability of deletion state

p_amp: numeric; Joint posterior probability of amplification states (2:1, 3:1)

p_bamp: numeric; Joint posterior probability of biallelic amplification state

p_bdel: numeric; Joint posterior probability of biallelic deletion state

LLR: numeric; Log-likelihood ratio of all data

LLR_y: numeric; Log-likelihood ratio of allele data

LLR_x: numeric; Log-likelihood ratio of expression data

n_genes: integer; Number of genes in the segment

n_snps: integer; Number of SNPs in the segment

component: integer; Component ID

LLR_sample: numeric; Log-likelihood ratio in the sample where the CNV has the highest LLR

seg_length: integer; Segment length in bp

seg_cons: character; Consensus segment ID

n_states: integer; Number of CNV states

cnv_states: character; CNV states

Clone assignments

cell: character; Cell ID

clone_opt: integer; Maximum a posteriori clone assignment

GT_opt: character; Maximum a posteriori genotype

p_opt: numeric; Maximum a posteriori clone probability

p_{k}: numeric; Posterior probability of cell beloning to clone k

p_x_{k}: numeric; Posterior probability of cell belonging to clone k given expression data

p_y_{k}: numeric; Posterior probability of cell belonging to clone k given allele data

p_cnv: numeric; Posterior probability of cell belonging to an aneuploid clone

p_cnv_x: numeric; Posterior probability of cell belonging to an aneuploid clone given expression data

p_cnv_y: numeric; Posterior probability of cell belonging to an aneuploid clone given allele data

compartment_opt: character; Maximum a posteriori compartment (tumor vs normal) assignment