Metadata Joins
Load Sample Metadata
import pandas as pd
# Load metadata
metadata = pd.read_csv('sample_info.csv', index_col=0)
# Metadata should have samples as rows, attributes as columns
# Index should match count matrix column names
Basic Join
import pandas as pd
# Count matrix: genes x samples
counts = pd.read_csv('counts.tsv', sep='\t', index_col=0)
# Metadata: samples x attributes
metadata = pd.read_csv('metadata.csv', index_col=0)
# Ensure sample order matches
common_samples = counts.columns.intersection(metadata.index)
counts = counts[common_samples]
metadata = metadata.loc[common_samples]
# Verify alignment
assert all(counts.columns == metadata.index)
Handle Sample Name Mismatches
def harmonize_sample_names(counts, metadata):
'''Match sample names between counts and metadata.'''
count_samples = set(counts.columns)
meta_samples = set(metadata.index)
common = count_samples & meta_samples
- meta_samples
- count_samples
if only_counts:
print(f'Samples in counts but not metadata: {only_counts}')
if only_meta:
print(f'Samples in metadata but not counts: {only_meta}')
counts = counts[sorted(common)]
metadata = metadata.loc[sorted(common)]
return counts, metadata
counts, metadata = harmonize_sample_names(counts, metadata)
Flexible Sample Name Matching
def fuzzy_match_samples(counts, metadata):
'''Try to match sample names with common transformations.'''
count_cols = counts.columns.tolist()
meta_idx = metadata.index.tolist()
# Try exact match first
if set(count_cols) == set(meta_idx):
return counts, metadata
# Common transformations
transformations = [
lambda x: x.replace('_', '-'),
lambda x: x.replace('-', '_'),
lambda x: x.split('_')[0],
lambda x: x.replace('.bam', ''),
lambda x: x.upper(),
lambda x: x.lower(),
]
for transform in transformations:
transformed = {transform(c): c for c in count_cols}
matches = {m: transformed[transform(m)] for m in meta_idx if transform(m) in transformed}
if len(matches) == len(meta_idx):
print(f'Matched using transformation')
counts = counts[[matches[m] for m in meta_idx]]
return counts, metadata
raise ValueError('Could not match sample names')
Add Gene Annotations
import mygene
def add_gene_annotations(counts, fields=['symbol', 'name', 'type_of_gene']):
'''Add gene annotation columns to count matrix.'''
mg = mygene.MyGeneInfo()
clean_ids = [g.split('.')[0] for g in counts.index]
results = mg.querymany(clean_ids, scopes='ensembl.gene',
fields=fields, species='human', as_dataframe=True)
# Merge annotations
results = results.reset_index().rename(columns={'query': 'gene_id'})
counts_reset = counts.reset_index().rename(columns={counts.index.name: 'gene_id'})
counts_reset['clean_id'] = counts_reset['gene_id'].str.split('.').str[0]
annotated = counts_reset.merge(
results[['gene_id'] + fields].drop_duplicates(),
left_on='clean_id', right_on='gene_id', how='left', suffixes=('', '_anno'))
annotated = annotated.drop(['clean_id', 'gene_id_anno'], axis=1, errors='ignore')
annotated = annotated.set_index('gene_id')
return annotated
R: Create DESeq2 Data
library(DESeq2)
# Load data
counts <- read.delim('counts.tsv', row.names=1)
metadata <- read.csv('metadata.csv', row.names=1)
# Ensure matching samples
common <- intersect(colnames(counts), rownames(metadata))
counts <- counts[, common]
metadata <- metadata[common, , drop=FALSE]
# Create DESeqDataSet
dds <- DESeqDataSetFromMatrix(
countData=as.matrix(counts),
colData=metadata,
design=~condition # Adjust to your design
)
R: Create edgeR DGEList
library(edgeR)
# Load data
counts <- read.delim('counts.tsv', row.names=1)
metadata <- read.csv('metadata.csv', row.names=1)
# Match samples
common <- intersect(colnames(counts), rownames(metadata))
counts <- counts[, common]
metadata <- metadata[common, , drop=FALSE]
# Create DGEList
y <- DGEList(counts=as.matrix(counts), group=metadata$condition)
y$samples <- cbind(y$samples, metadata)
Create AnnData with Metadata
import anndata as ad
import pandas as pd
def create_annotated_anndata(counts, sample_metadata, gene_metadata=None):
'''Create AnnData object with full metadata.'''
# AnnData expects samples as rows
adata = ad.AnnData(X=counts.T)
# Add sample metadata (obs)
adata.obs = sample_metadata.loc[counts.columns].copy()
# Add gene metadata (var)
if gene_metadata is not None:
adata.var = gene_metadata.loc[counts.index].copy()
else:
adata.var_names = counts.index
return adata
# Usage
adata = create_annotated_anndata(counts, metadata)
adata.write_h5ad('annotated_counts.h5ad')
Validate Metadata
def validate_metadata(counts, metadata, required_columns=['condition']):
'''Check metadata validity.'''
issues = []
# Check sample overlap
count_samples = set(counts.columns)
meta_samples = set(metadata.index)
if count_samples != meta_samples:
missing = count_samples - meta_samples
extra = meta_samples - count_samples
if missing:
issues.append(f'Samples missing metadata: {missing}')
if extra:
issues.append(f'Extra metadata samples: {extra}')
# Check required columns
for col in required_columns:
if col not in metadata.columns:
issues.append(f'Missing required column: {col}')
elif metadata[col].isna().any():
n_na = metadata[col].isna().sum()
issues.append(f'Column {col} has {n_na} missing values')
if issues:
for issue in issues:
print(f'WARNING: {issue}')
return False
print('Metadata validation passed')
return True
Merge Multiple Metadata Files
def merge_metadata_files(files, on='sample_id'):
'''Merge multiple metadata files.'''
dfs = [pd.read_csv(f) for f in files]
merged = dfs[0]
for df in dfs[1:]:
merged = merged.merge(df, on=on, how='outer')
return merged.set_index(on)
# Usage
metadata = merge_metadata_files(['clinical.csv', 'sequencing.csv', 'qc.csv'])
Related Skills
- expression-matrix/counts-ingest - Load count data
- expression-matrix/gene-id-mapping - Convert gene IDs
- differential-expression/deseq2-basics - Downstream analysis
- single-cell/preprocessing - Single-cell metadata handling
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