Man pages for genevol-usp/hlaseqlib
R utility functions for the HLA RNAseq project
| calc_genotyping_accuracy | Calculate genotyping accuracy from RNA-seq calls. |
| counts_to_fpkm | Convert read counts to FPKM |
| counts_to_tpm | Convert read counts to TPM |
| fpkm_to_tpm | Convert FPKM to TPM |
| get_gencode_coords | Parse Gencode gtf files into a data.frame of ids and... |
| hla_apply_zigosity_threshold | Apply zigosity threshold to expression estimates |
| hla_compile_index | Process HLA alignment data in *.nuc files and return a... |
| hla_genotype | Infer HLA genotypes from RNA-seq quantifications. |
| hla_read_alignment | Process HLA alignment data in *.nuc or *.gen files and return... |
| hla_readtx | Read hlaTX output file |
| hla_trimnames | Trim HLA allele names to the specified number of fields. |
| phase_hla | Pfase HLA alleles given distances to 1000G haplotypes |
| read_phase | Read in PHASE output file |
| read_phase_probs | Read in PHASE output file |
| read_qtltools | Read in QTLtools output from secondary chunk analysis |
| read_qtltools_rtc | Read in QTLtools rtc output |
