Commit f74a72d0 authored by RomainFeron's avatar RomainFeron
Browse files

Updated doc

parent 4e674e5f
......@@ -121,7 +121,7 @@ class Depth: public Analysis {
*
* Compute minimum, maximum, median, and average depth for all markers retained in process_marker. \n
* Generate a tabulated output file with columns: \n
* Individual | Group | Markers | Retained | Min_depth | Max_depth | Median_depth | Average_depth
* Individual | Group | Reads | Markers | Retained | Min_depth | Max_depth | Median_depth | Average_depth
*/
void generate_output();
......
......@@ -54,7 +54,7 @@ struct DistribResults {
*
* Compute the distribution of markers between two groups. \n
* After all markers are processed, generate a tabulated output file with columns: \n
* Group1 | Group2 | Markers | P | Signif | Bias
* Group1 | Group2 | Markers | P | P corrected | Signif | Bias
*
*/
......@@ -97,7 +97,7 @@ class Distrib: public Analysis {
*
* Compute probability of association with group for each combination of number of individuals from group1 and group2. \n
* Generate a tabulated output file with columns: \n
* Group1 | Group2 | Markers | P | Signif | Bias
* Group1 | Group2 | Markers | P | P corrected | Signif | Bias
*/
void generate_output();
......
......@@ -73,7 +73,7 @@ struct MapResults {
* Align all markers from a markers depth table to an assembly using the "mem" algorithm implemented in the BWA library (https://github.com/lh3/bwa). \n
* For all aligned markers, compute probability of association with groups and group bias (bias score between -1 and 1). \n
* After all markers are processed, generate a tabulated output file with columns: \n
* Contig | Position | Length | Marker_id | Bias | P | Signif
* Contig | Position | Length | Marker_id | Bias | P | P corrected | Signif
*
*/
......
......@@ -86,7 +86,8 @@ class Marker {
/*!
* \brief Output a marker in FASTA format
*
* Generate a FASTA header line with format "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_mindepth:<minimum depth to consider a marker present in the analysis"
* Generate a FASTA header line with format
* "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_pcorr:<corrected p-value>_mindepth:<minimum depth to consider a marker present in the analysis>"
* followed by the marker's sequence on a single line.
*
* \param output_file Output file stream
......
......@@ -54,7 +54,8 @@ struct SignifResults {
*
* Find all markers significantly associated with groups. \n
* After all markers are processed, significant markers are output either as a markers depth table (ID | Sequence | Depth in individual 1 | .... | Depth in individual N)
* or in a FASTA file with headers formatted as "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_mindepth:<minimum depth to consider a marker present in the analysis"
* or in a FASTA file with headers formatted as
* "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_pcorr:<corrected p-value>_mindepth:<minimum depth to consider a marker present in the analysis>"
*
*/
......@@ -98,7 +99,8 @@ class Signif: public Analysis {
* Apply Bonferroni correction (if not disabled) to assess significance of association with groups. \n
* Export markers significantly associated with group to a file, either: \n
* - a markers depth table, i.e. tabulated file for columns "ID | Sequence | Depth in individual 1 | .... | Depth in individual N"
* - a FASTA file with headers formatted as "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_mindepth:<minimum depth to consider a marker present in the analysis"
* - a FASTA file with headers formatted as
* "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_pcorr:<corrected p-value>_mindepth:<minimum depth to consider a marker present in the analysis>"
*/
void generate_output();
......
......@@ -39,7 +39,8 @@
*
* Filter markers based on presence in individuals from each group \n
* Markers are output either as a markers depth table (ID | Sequence | Depth in individual 1 | .... | Depth in individual N)
* or in a FASTA file with headers formatted as "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_mindepth:<minimum depth to consider a marker present in the analysis"
* or in a FASTA file with headers formatted as
* "<id>_<group1:count>_<group2:count>_p:<p-value of association with group>_pcorr:<corrected p-value>_mindepth:<minimum depth to consider a marker present in the analysis>"
*
*/
......
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