This function computes loads in a set of promoter capture Hi-C files (pcHi-C). This is a tab delimited file that contains the following mandatory columns

  1. ensg - Ensembl gene id for gene

  2. name - Gene name

  3. biotype - Gene biotype from ensembl e.g. protein_coding

  4. strand - Gene strand

  5. baitChr - Bait (A captured restriction fragment) chromosome

  6. baitStart - Bait fragment start

  7. baitEnd - Bait fragment end

  8. baitID - Bait fragment ID should match ID in digest file

  9. baitName - Free text of what is captured - deprecated.

  10. oeChr - 'Other end' (Promoter interacting restriction fragment) chromosome

  11. oeStart - 'Other end' fragment start

  12. oeEnd - 'Other end' fragment end

  13. oeID - 'Other end' fragment ID should match ID in digest file

  14. oeName - Free text of what is interacting - deprecated.

Additional columns contain CHiCAGO scores for one or more columns.

This function computes loads in a set of promoter capture Hi-C files (pcHi-C). This is a tab delimited file that contains the following mandatory columns

  1. ensg - Ensembl gene id for gene

  2. name - Gene name

  3. biotype - Gene biotype from ensembl e.g. protein_coding

  4. strand - Gene strand

  5. baitChr - Bait (A captured restriction fragment) chromosome

  6. baitStart - Bait fragment start

  7. baitEnd - Bait fragment end

  8. baitID - Bait fragment ID should match ID in digest file

  9. baitName - Free text of what is captured - deprecated.

  10. oeChr - 'Other end' (Promoter interacting restriction fragment) chromosome

  11. oeStart - 'Other end' fragment start

  12. oeEnd - 'Other end' fragment end

  13. oeID - 'Other end' fragment ID should match ID in digest file

  14. oeName - Free text of what is interacting - deprecated.

Additional columns contain CHiCAGO scores for one or more columns.

make_pchic(
  f,
  chic_thresh = 5,
  biotype.filter = "protein_coding",
  remove.trans.contacts = TRUE
)

Arguments

f

a scalar representing file name of pcHi-C file
chic_thresh

scalar representing CHiCAGO threshold for calling a significant interaction. Default is set to 5.
biotype.filter

scalar/vector of characters representing a biotype filter. Default is set to 'protein_coding'
remove.trans.contacts

a boolean on whether to remove interaction between chromosomes. Default is set to TRUE.

Value

list of data.tables where each data.table has three columns ensg,fragid and chic.score