View source: R/post_process_rnaseq_align.R
post_process_rnaseq_align | R Documentation |
Joins individual sample files into one tsv file. Also converts ucsc names to hgnc_symbol|entrez_ids and outputs the gene level counts.
post_process_rnaseq_align(
this_script_path = "",
input_file_paths,
output_dir,
ref = "grch38",
gene_biotypes = c("protein_coding", "from AnnotationDbi", "IG_C_gene", "IG_D_gene",
"IG_J_gene", "IG_V_gene", "TR_C_gene", "TR_D_gene", "TR_J_gene", "TR_V_gene"),
file_prefix = "",
output_transcript_matrix = TRUE,
output_hgnc_matrix = TRUE,
output_entrez_id_matrix = FALSE,
output_piped_hugo_entrez_id_matrix = FALSE,
output_upper_quartile_norm = TRUE,
output_log2_upper_quartile_norm = TRUE,
output_conversion_table = TRUE,
counts_or_tpm = "counts",
sample_key = "Run_ID"
)
this_script_path |
Path to script that runs this function for documentation purposes |
input_file_paths |
Named character vector of paths to the pipeline output data. Samples will be named by the names of the vector. If not named thye will be named after the quant file. |
output_dir |
Path to the output folder. |
ref |
options 'grch38' with ensemble output or 'hg38' with ucsc output |
gene_biotypes |
The type of biomaRt gene_biotypes that should be output to the gene level output. |
file_prefix |
Output files will have this prefix string appended to them |
output_transcript_matrix |
T/F |
output_hgnc_matrix |
T/F |
output_entrez_id_matrix |
T/F |
output_piped_hugo_entrez_id_matrix |
T/F |
output_upper_quartile_norm |
T/F |
output_log2_upper_quartile_norm |
T/F |
counts_or_tpm |
'counts' or 'tpm' |
sample_key |
String to name the sample identifier column. |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ post_process_rnaseq_align ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A vector of paths to the files.
Other mart:
get_biomart_grch38_path()
,
get_biomart_hg38_path()
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