Open shashwatsahay opened 2 years ago
Hi,
Is there a constructor which directly converts a bed file into a QDNAseq counts object.
I have a manually normalised count dataframe that I would like to convert into QDNAseq counts object.
chr bin_start bin_end bin_len bin_ind normalised_counts counts 1 1 1000000 999999 1 -1.0 -1.0 1 1000000 2000000 1000000 2 1.9563313228679595 6471.0 1 2000000 3000000 1000000 3 1.7959808612440193 5831.0 1 3000000 4000000 1000000 4 2.1815908104054 5006.0 1 4000000 5000000 1000000 5 1.8522823862440945 4386.0 1 5000000 6000000 1000000 6 1.7374568288854002 4411.0 1 6000000 7000000 1000000 7 2.0295699960076092 5871.0 1 7000000 8000000 1000000 8 1.7201969234365184 5333.0 1 8000000 9000000 1000000 9 2.1330930294195602 5832.0 1 9000000 10000000 1000000 10 1.7651345542717536 6528.0 1 10000000 11000000 1000000 11 1.8698060381177264 5774.0 1 11000000 12000000 1000000 12 1.9361234254467337 5388.0 1 12000000 13000000 1000000 13 1.8358008110726192 5064.0 1 13000000 14000000 1000000 14 -1.0 -1.0 1 14000000 15000000 1000000 15 1.7447801574292559 4387.0 1 15000000 16000000 1000000 16 1.7856350898568385 5841.0 1 16000000 17000000 1000000 17 1.8243780648454042 5990.0 1 17000000 18000000 1000000 18 1.8388992465260687 5499.0 1 18000000 19000000 1000000 19 1.7154621040335325 5088.0 1 19000000 20000000 1000000 20 1.7935685094126652 6261.0 1 20000000 21000000 1000000 21 2.2186218332868144 6120.0 1 21000000 22000000 1000000 22 1.716944375105414 5763.0 1 22000000 23000000 1000000 23 1.811195901200985 6212.0 1 23000000 24000000 1000000 24 1.9318113465481888 6720.0 1 24000000 25000000 1000000 25 2.018586800954148 5174.0 1 25000000 26000000 1000000 26 1.900484277627135 5428.0 1 26000000 27000000 1000000 27 1.933725976174956 6113.0 1 27000000 28000000 1000000 28 1.957852620181039 6715.0 1 28000000 29000000 1000000 29 1.7993508052571678 5227.0 1 29000000 30000000 1000000 30 1.827352659926606 5063.0 1 30000000 31000000 1000000 31 1.8821740975232326 5123.0
Hi,
Is there a constructor which directly converts a bed file into a QDNAseq counts object.
I have a manually normalised count dataframe that I would like to convert into QDNAseq counts object.