diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 16 |
1 files changed, 9 insertions, 7 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fbe78d5d..3deaa655 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -168,13 +168,13 @@ class Markers(object): for marker, p_value in itertools.izip(self.markers, p_values): marker['p_value'] = p_value - if math.isnan(marker['p_value']): - print("p_value is:", marker['p_value']) - marker['lod_score'] = -math.log10(marker['p_value']) - #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values - marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 - - + if math.isnan(marker['p_value']) or marker['p_value'] <= 0: + marker['lod_score'] = 0 + marker['lrs_value'] = 0 + else: + marker['lod_score'] = -math.log10(marker['p_value']) + #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values + marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 class HumanMarkers(Markers): @@ -184,6 +184,7 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() + #print("splat:", splat) marker = {} marker['chr'] = int(splat[0]) marker['name'] = splat[1] @@ -203,6 +204,7 @@ class HumanMarkers(Markers): # #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values # marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + print("p_values2:", p_values) super(HumanMarkers, self).add_pvalues(p_values) with Bench("deleting markers"): |